Re: [Freesurfer] mri_watershed Error: indices out of bounds

2018-03-31 Thread Bruce Fischl
searched the email archive and found this thread: > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22=newest=1 > My problem seems identical to the one described by initial poster. > The suggestion was

[Freesurfer] mri_watershed Error: indices out of bounds

2018-03-30 Thread Darko Komnenić
+Error\%3A+indices+out+of+bounds%22=newest=1 My problem seems identical to the one described by initial poster. The suggestion was to try the following command: set mdir=$SUBJECTS_DIR/$subject/mri mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz $mir/nu.mgz When I tried

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-04-06 Thread Ani Varjabedian
Hello Edgar, We think we were able to isolate the problem. Version 5.1 is failing to apply the talairach transform to the nu.mgz. It gets computed and applied to the orig.mgz but then not transferred during the next step. When mri_normalize tries to run without this information, it fails,

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-04-02 Thread Ani Varjabedian
Hello Edgar, I am going to be looking at your case and seeing if I can replicate the error. I have your .nii file and will run it through our processing stream here, but could you send me your subject folder so that I can look through your files/logs to give me some more information? You

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-04-02 Thread Edgar Busovaca
Hello Bruce, I just wanted to touch base regarding the Indices_oob.nii subject I had sent to MGH. Were you by any chance able to detect the issue with running recon-all on this subject. Thanks in advance for taking a look at this. Best regards, Edgar Busovaca

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-03-31 Thread Ani Varjabedian
Hello Edgar, Could you upload the whole subject folder? I could try to run it through recon all here and see if I can reproduce the error. It would also allow me to look through your log files to see if I can spot anything that could be causing this issue. You can use FileDrop2.0 if the

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-03-25 Thread Edgar Busovaca
Hello Bruce, I took a look at the file with freeview and I can't identify anything peculiar about the data. The file is named Indices_oob.nii and has been uploaded to /transfer/incoming on the FTP file exchange server. Thank you for your swift reply and in advance for your time. Best regards,

Re: [Freesurfer] mri_watershed Error: indices out of bounds

2015-03-24 Thread Bruce Fischl
Hi Edgar the LINE SEARCH thing is not a real problem. I've never seen indices out of bounds before though. Is there anything strange about your dataset? Does freeview display it properly (that is, are what freeview thinks the RAS dirs the correct anatomical ones)? If you upload the dataset

[Freesurfer] mri_watershed Error: indices out of bounds

2015-03-24 Thread Edgar Busovaca
Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE

[Freesurfer] mri_watershed Error: indices out of bounds

2015-03-24 Thread Edgar Busovaca
Dear Freesurfer users, I have attempted to process a subject (.nii type input) through recon-all -all, but for some reason the processing gambit is terminated early ( during the skullstrip). During skullstripping the following warning appears twice: IFLAG= -1 LINE SEARCH FAILED. SEE