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MRIQC T1w Classifier #699
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Hi @n2parker, you should be seeing one column added into the T1w.csv file. Could you share that T1w.csv file with me so that I try to reproduce? |
Hi,
sure here is the file.
Nadine Parker, M.Sc.
Graduate Student, Paus Lab
Rotman Research Institute, Baycrest
Institute of Medical Science
University of Toronto
Email: nparker@research.baycrest.org
Alternate email: nadine.parker@mail.utoronto.ca
Phone: (416) 785-2500 ext: 3130 <%28416%29%20785-2500%20ext%3A%203425>
…On 12 March 2018 at 17:11, Oscar Esteban ***@***.***> wrote:
Hi @n2parker <https://github.com/n2parker>, you should be seeing one
column added into the T1w.csv file. Could you share that T1w.csv file with
me so that I try to reproduce?
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Hi, the attachment seems to have gotten lost from the reply. Also, I am wondering if you were using an outdated version of MRIQC, in which you would need to use the |
I did try the -o flag and it wasn't recognized. |
Nadine Parker, M.Sc.
Graduate Student, Paus Lab
Rotman Research Institute, Baycrest
Institute of Medical Science
University of Toronto
Email: nparker@research.baycrest.org
Alternate email: nadine.parker@mail.utoronto.ca
Phone: (416) 785-2500 ext: 3130 <%28416%29%20785-2500%20ext%3A%203425>
…On 12 March 2018 at 18:48, Oscar Esteban ***@***.***> wrote:
Hi, the attachment seems to have gotten lost from the reply.
Also, I am wondering if you were using an outdated version of MRIQC, in
which you would need to use the -o flag to indicate where to store the
predictions. Could you try with latest?
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I'm afraid that github does not accept attachments via email :(. Could you write directly to my email (oesteban@stanford.edu) |
Hi, |
I ran into a similar issue using mriqc with singularity on the same HPC server. Like @n2parker, I received no warnings or errors when running Replicating the original issueThe command I ran is below. Note that:
$ PYTHONPATH="" singularity exec \
-H $SCRATCH/sing_home \
-B $SCRATCH/BIDS/mriqc_clf/CN_BIDS_output:/output \
$HOME/BIDS_apps/mriqc/poldracklab_mriqc_0.11.0-2018-06-05-b7b338730c42.img \
mriqc_clf --load-classifier \
-X /output/T1w.csv \ To check whether T1w.csv was modified, I ran As mentioned by @oesteban above, I tried the Further troubleshootingI re-ran the command with > 2018-07-05 18:09:40,840 mriqc.classifier:INFO Results saved as /scratch/a/agraff/channa13/sing_home/mclf_run-20180705-180940* Navigating to $ cat /scratch/a/agraff/channa13/sing_home/mclf_run-20180705-180940_data-unseen_pred.csv | head -n 5
> subject_id,prob_y,pred_y
002S0295,0.147785410865424,0
002S0413,0.3250233296316222,0
002S1261,0.2381351524431868,0
002S1280,0.308822544009952,0 The .csv contains 3 columns: Remaining issuesBased on the comment from @oesteban here, it seems like the expected behaviour of If the
Note that a new |
Hi @n2parker, @nathankchan. I can confirm all that @nathankchan described, and add some details:
I'll work in making the interface of the classifier more intuitive. I agree it is quite a mess at this moment. Sorry about that. |
I have MRIQC Outputs of approximately 1000 T1w images. I would like to produce the default T1w classifier using the mriqc_clf command. Since I'm working with singularity on a HPC server I use the following command after loading the singularity module:
with the exception of the following minor warning there are no errors.
No new output is generated after the command is run and no new additional column is created in the T1w.csv. I'm not sure what has gone wrong here?
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