Re: [Freesurfer] recon-all error

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 > > Chindh

[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 /autofs/clu

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,

[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: mr

[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 /cluster/manoach/milt

[Freesurfer] QC Montages error

td_lightbox1.png + > $((gap)) tstd_lightbox2.png + $((gap)) tstd_lightbox3.png - $((gap)) > tstd_lightbox4.png + $((gap)) tstd_lightbox5.png + $((gap)) > tstd_lightbox6.png tstd_all.png > > Cannot open tmean_lightbox1.png for reading > /autofs/cl

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 > > > F

[Freesurfer] QC Montages error

tbox6.png tmean_all.png mv: cannot stat `/autofs/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 o

[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

Re: [Freesurfer] launchpad help

ueue names > are also 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 t

[Freesurfer] launchpad help

geant -l nodes=1:opteron -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 Neuro

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

-zero exit > status. > > cheers > 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 >> d

[Freesurfer] Error in recon-all on seychelles

Execution terminated Exit_status=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] 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 'Se

[Freesurfer] Segmentation Fault

nks! 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/freesu

[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

MST08 -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 > > Chind

Re: [Freesurfer] Abblocked Setup

It is going to assume that the first 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 alternati

[Freesurfer] abblocked Setup

tions 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 P

[Freesurfer] Abblocked Setup

tions 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 P

Re: [Freesurfer] spmregister error

??? Undefined function or variable 'VG'. >> >> >> ??? Undefined function or method 'spm_vol' for input arguments of type 'char'. >> ??? Undefined function or variable 'VF'. >> >> INFO: ignore warnings about scalefactor

Re: [Freesurfer] spmregister error

spm2 added in your startup.m file and are you using matlab 7.1 (required by spm2)? > > doug > > Chindhuri Selvadurai wrote: >> 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

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 oth