Re: [Freesurfer] recon-all error

an analysis of an existing subject, then omit all -i flags. I deleted all the files, and re-ran, and it still didn't work, so I then deleted the -i flag and tried again. In the log file, it says that you did not run it with the -i. Check your command line. doug Chindhuri Selvadurai wrote

[Freesurfer] recon-all error

Hello, I am having trouble doing a recon-all of my data. pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-15-01.dcm -mail chin...@nmr.mgh.harvard.edu' Here is the error: ERROR: no run data found in

Re: [Freesurfer] mri_glmfit .nii files

. By default this is compressed nifti (nii.gz). Both nii and nii.gz store the same information. The nii.gz is compressed, so you save some space. doug Chindhuri Selvadurai wrote: Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz

[Freesurfer] mri_glmfit .nii files

Hi freesurfers, I am trying to run an analysis right now, however, after using isxconcat, I am only finding ces.nii.gz files in the output directory and no .nii files. output dir: /cluster/manoach/milton/subjects/group_analysis/volume/m1 subjects_dir: /cluster/manoach/milton/subjects command:

[Freesurfer] isxconcat-sess missing dof file

Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o

[Freesurfer] QC Montages error

/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/all_lightboxes/*all*': No such file or directory rm: cannot remove `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/0*/lightboxes/': No such file or directory Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab

Re: [Freesurfer] QC Montages error

Hello, I have tried troubleshooting this problem in various ways, but I am still not able to figure out the problem. Does anyone have any idea? Thank you! I am getting an error when using a script that combines these 3 actions: preproc.sh std_map_qc_montages.bash put_tpef.bash

[Freesurfer] preprocessing qc

Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] QC Montages error

or directory rm: cannot remove `/autofs/cluster/manoach/AS/RespMon12C/subjects/RMAUT021/bold/0*/lightboxes/': No such file or directory Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

Re: [Freesurfer] launchpad help

different than seychelles. There is no sergeant queue. Read: https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: Hello, I am trying to do recon-all using launchpad, and I am not sure how to fix the error I am getting. I checked IT's

[Freesurfer] launchpad help

-r n /pbs/chinsel/pbsjob_3 qsub: Unknown queue MSG=cannot locate queue FATAL: qsub call failed. Check above for error messages. I'm also not getting any e-mails. Is there a way to check an error log like on seychelles? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos

[Freesurfer] Error in recon-all on seychelles

=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01 Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

Re: [Freesurfer] Error in recon-all on seychelles

Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote: Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could

Re: [Freesurfer] Segmentation Fault

Not happening anymore, thanks! Hi Chinduri, is this still happening? I can't replicate. doug Chindhuri Selvadurai wrote: Hi all, We are trying to run individual analyses on several subjects, and we keep getting a 'Segmentation Fault.' We have run other subjects with the same command

[Freesurfer] Segmentation Fault

, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] fs stable 4 vs 5; preproc-sess

Hello, We have a question about preprocessing in fs4 compared to fs5. We used the preproc-sess command without specifying -surface or volume and did all our processing and analysis in fs5. I believe in fs4 you didn't have to specify this. Do you think this is a problem for doing both surface and

Re: [Freesurfer] Abblocked Setup

-hemi -lh -analysis mandy_mst_v_mct_lh -call I think perhaps it would be better for us to switch to the block design to make things simpler? Thanks!! Chindhuri sfa-sess is depricated now (should not even be in there). Use selxavg3-sess. doug Chindhuri Selvadurai wrote: Hi Doug

[Freesurfer] abblocked Setup

will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric

Re: [Freesurfer] Abblocked Setup

condition is ON. This does not matter for the F-tests above, but will affect the sign of the sine component. doug Chindhuri Selvadurai wrote: Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't

Re: [Freesurfer] spmregister error

command line, directory you ran it from, SUBJECTS_DIR, and terminal output? doug Chindhuri Selvadurai wrote: The path to spm2 was not originally in my startup.m file, but even when I added it, it didn't work. I am using 7.8, but I tried to change my cshrc file back to 7.1 however, once I ran

Re: [Freesurfer] spmregister error

Hello, I am getting the same error that was discussed in the attached thread, however, the addition of the path line did not work for me. I am also not sure if we should be using spm5 since all in the past we have been using spm2. It presents this error when running under my name, but not for