Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Cortical thickness
by Joshua deSouza 08 Jun '13

08 Jun '13

Hello Doug, Each individuals subject data has already been smoothed by 5 10 15 20 and 25 through the qache function during the initial processing. I'm a little confused now. I thought that the mri_preproc would use the non-smoothed values of the subjects and create an mgh file. After which I smooth the mgh file and then use mri_glmfit to analyse it according to the contrasts. If the above is not the case and the subject data has already been smoothed, then what should I do if I wish my final mgh file to have a smoothing value of 15 before doing a glmfit on it? Thank you, Joshua On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza <desouzajoshua00(a)gmail.com>wrote: > Hello Doug, > > Each individuals subject data has already been smoothed by 5 10 15 20 and > 25 through the qache function during the initial processing. > > I'm a little confused now. I thought that the mri_preproc would use the > non-smoothed values of the subjects and create an mgh file. After which I > smooth the mgh file and then use mri_glmfit to analyse it according to the > contrasts. > > If the above is not the case and the subject data has already been > smoothed, then what should I do if I wish my final mgh file to have a > smoothing value of 15 before doing a glmfit on it? > > Thank you, > > Joshua > > On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > >> >> Hi Joshua, when you add --fwhm 15 to the command line you are instructing >> mri_glmfit to smooth by 15mm. Is this what you want? Or is the data >> already smoothed? >> doug >> >> >> >> On 6/3/13 12:26 AM, Joshua deSouza wrote: >> >> Hi Doug, >> >> The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C >> t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir >> >> I am doing a whole hemisphere analysis and am measuring cortical >> thickness. I do not have my own mask but I have doubts about the mask that >> has been produced because from previous studies, there has been significant >> thinning in the area around the hippocampus and parts of it are being left >> out in the mask, such as the para-hippocampal region. >> >> Regards >> >> Joshua >> >> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > wrote: >> >>> >>> The residual FWHM is measured from the data itself. You apply a certain >>> amount of smoothing, but there is already some smoothness to the data, so >>> the final fwhm is a combination of what is already there and what you >>> apply. A fwhm of 47 is huge and may indicate that something is wrong. What >>> is the input? cortical thickness? Are you using your own mask or is this a >>> whole hemisphere analysis? >>> >>> doug >>> >>> >>> >>> >>> >>> >>> On 6/2/13 10:29 PM, Joshua deSouza wrote: >>> >>> Hello Doug, >>> >>> Thank you for your quick replies to my queries. Really appreciate it. >>> >>> I have found the files containing the cortical thickness values. Thank >>> you. I assume that the order in which they follow are based on the fsgd >>> file and the cluster annotation numbers. >>> >>> I was just slightly confused about the residual fwhm. I have already >>> done a smoothing of 15 on the file and have recieved a residual value of >>> 47, which I assume is extremely large. Since I'm finding out values for the >>> entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of >>> 47. Could you please tell me what the residual values mean? What do you >>> recommend I do? Is there anything I can read up on to find out more about >>> this? (Please pardon my questions if they seem a little trivial) >>> >>> Thank you >>> >>> Joshua >>> >>> On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve < >>> greve(a)nmr.mgh.harvard.edu> wrote: >>> >>>> >>>> This file is always created by mri_glmfit-sim. It might be named >>>> something different depending on your parameters (should always end in >>>> y.ocn.dat) >>>> doug >>>> >>>> >>>> On 6/2/13 3:57 AM, Joshua deSouza wrote: >>>> >>>> Hi Doug, >>>> >>>> This file that your saying, will be created after glmfit-sim is done >>>> using the cache function and a threshold of 1.3 and absolute ,with y being >>>> the fsgd file? Am I understanding this correctly? >>>> >>>> Thank you >>>> >>>> Joshua >>>> >>>> On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve < >>>> greve(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> There should be a file called something like cache.th13.abs.y.ocn.dat. >>>>> This will have a column for each cluster and a row for each subject. >>>>> The >>>>> value in the row will be the input for each subject. >>>>> doug >>>>> >>>>> On 05/30/2013 11:21 PM, Joshua deSouza wrote: >>>>> > Hello everyone, >>>>> > >>>>> > Please pardon my rather simple question >>>>> > >>>>> > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf >>>>> > with a few others after the analysis.As I know, I do not have to >>>>> > create ROIs in order to do this. I also understand that doing a >>>>> > multiple comparison analysis just compares the regions of importance >>>>> > and evaluates them giving the most resilient cluster depending on the >>>>> > threshold. So, this does not give a thickness estimate. I would like >>>>> > to know how do I get the cortical thickness values from the results? >>>>> > If so, can I do it after glmfit? >>>>> > >>>>> > And thanks Doug for your help in the other questions that I had prior >>>>> > to this! >>>>> > >>>>> > Thank you >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > Freesurfer mailing list >>>>> > Freesurfer(a)nmr.mgh.harvard.edu >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom >>>>> it is >>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>> e-mail >>>>> contains patient information, please contact the Partners Compliance >>>>> HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>> you in error >>>>> but does not contain patient information, please contact the sender >>>>> and properly >>>>> dispose of the e-mail. >>>>> >>>>> >>>> >>>> >>> >>> >> >> >

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Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
by Douglas N Greve 07 Jun '13

07 Jun '13

Hi Pablo, please respond to the list and not to us directly. Please just cut and paste the text of the error into the email. thanks doug On 06/06/2013 12:30 PM, pablo najt wrote: > Thank you for your quick response. I have re run the installation but > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer > bert rh pial_ commands. > Please see attach for the detailed errors. > Best, > Pablo > > > > Date: Thu, 6 Jun 2013 12:01:22 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed} > > > > what command is not found? > > On 06/06/2013 11:58 AM, pablo najt wrote: > > > Hello I have a question regarding the installation/running FreeSurfer. > > > I have just completed the installation and got the confirmation that > > > Free surfer was installed. Please see snapshot. > > > However when I follow the steps for testing (*MailScanner has > detected > > > a possible fraud attempt from "connect.yale.edu" claiming to be* > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer > > > > <https://connect.yale.edu/owa/14.3.123.3/scripts/premium/redir.aspx?C=Alh1Yj…>), > > > > I always get "command not found". I was wondering if you would be > able > > > to help me. > > > Thanks, > > > Pablo > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the sender > and properly > > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

3 5

Hypointense lesions
by Fotiadis, Panagiotis 07 Jun '13

07 Jun '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

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mri_convert
by Ray, Siddharth 07 Jun '13

07 Jun '13

Hi free-surfer folks, I have some subjects with L-R header flipped in nifti's. Is it possible to flip the header using mri_convert so that I can have the right orientation information for subjects. Please let me know. Thanks, -Siddharth

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FS-FAST - ERROR: mapping surfaces
by preciado＠nmr.mgh.harvard.edu 07 Jun '13

07 Jun '13

I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh --------- Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 -> fsaverage) ERROR: mapping surfaces

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R: Re: R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Ok, now I think that I have downloaded the correct file. I try to rerun trac-all -prep and at the end I'll send you a feedback. Thanks, Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.18 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: mris resample: Command not found. This error is permanent after new patch download I dont know why your getting a file named "unknown". If you click this link you should be able to download a file called "mris_resample": ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/ Download it and place it in $FREESURFER_HOME/bin (Usually Applications/freesurfer/bin on Macs). Then make it executable by typing "chmod +x Applications/freesurfer/bin/mris_resample" on the command line. -Zeke If you go this this link On 06/07/2013 12:09 PM, stdp82(a)virgilio.it wrote: > Hi Zeke, thank you very much. > > I have download a file that named "unknown". > > I should rename it as "mris_resample"? > > > Stefano > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 7-giu-2013 18.02 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] mris resample: Command not found. This error is > permanent after new patch download > > Stefano, step 4 should be: > > "chmod +x $FREESURFER_HOME/bin/mris_resample" > > When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need > to see the to see the x's next to mris_resample just like you do with > all the other files in that directory. > > -Zeke > > > On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > during trac-all -prep I have this error: > > > > MRISregister() return, current seed 0 > > writing registered surface to > > > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > > expanding nbhd size to 1 > > mris_resample: Command not found. > > Darwin iMac > > > > I have performed my analysis by the following steps (as recommended by > > Zeke and Lilla): > > > > 1. download "unKnow" file (7.6 MB) at > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > > 2. put file in $FREESURFER/bin/ > > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > > I did not use this command) > > 5. start trac-all -prep > > 6. ERROR (in inter-reg step) > > > > What's happen? > > > > Thank you very much, > > > > > > Stefano > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi Zeke, thank you very much. I have download a file that named "unknown". I should rename it as "mris_resample"? Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

[iMac-di-Stefano:/Applications/freesurfer/bin] Stefano% ls -ltotal 4780656-rwxr-xr-x 1 root wheel 60776 Jan 29 00:20 #trac-all#-rwxr-xr-x 1 root wheel 27224 May 14 17:07 4dfptoanalyze-rwxr-xr-x 1 root wheel 12925 May 14 17:07 LongQdecTable.py-rwxr-xr-x@ 1 Stefano wheel 7581520 Jun 6 23:24 Unknown-rwxr-xr-x 1 root wheel 936 May 14 17:07 UpdateNeeded-rwxr-xr-x 1 root wheel 22628 May 14 17:07 analyzeto4dfp-rwxr-xr-x 1 root wheel 7660 May 14 17:07 aparc2feat-rwxr-xr-x 1 root wheel 15795 May 14 17:07 aparcstats2table-rwxr-xr-x 1 root wheel 4657 May 14 17:07 aparcstatsdiff-rwxr-xr-x 1 root wheel 7075840 May 14 17:07 applyMorph-rwxr-xr-x 1 root wheel 8927 May 14 17:07 aseg2feat-rwxr-xr-x 1 root wheel 23702 May 14 17:07 asegstats2table-rwxr-xr-x 1 root wheel 3450 May 14 17:07 asegstatsdiff-rwxr-xr-x 1 root wheel 2087 May 14 17:07 avi2talxfm-rwxr-xr-x 1 root wheel 2209 May 14 17:07 batchjobs-rwxr-xr-x 1 root wheel 5756 May 14 17:07 bblabel-rwxr-xr-x 1 root wheel 24890 May 14 17:07 bbregister-rwxr-xr-x 1 root wheel 14696 May 14 17:07 bedpostx_mgh-rwxr-xr-x 1 root wheel 13268 May 14 17:07 bet.fsl-rwxr-xr-x 1 root wheel 7144 May 14 17:07 beta2sxa-rwxr-xr-x 1 root wheel 7710 May 14 17:07 biasfield-rwxr-xr-x 1 root wheel 417 May 14 17:07 brec-rwxr-xr-x 1 root wheel 973 May 14 17:07 brec.awk-rwxr-xr-x 1 root wheel 10814 May 14 17:07 browse-minc-header.tcl-rwxr-xr-x 1 root wheel 2201 May 14 17:07 bugr-rwxr-xr-x 1 root wheel 1245 May 14 17:07 build_desikan_killiany_gcs.csh-rwxr-xr-x 1 root wheel 75584 May 14 17:07 check_siemens_dir-rwxr-xr-x 1 root wheel 2496 May 14 17:07 check_subject-rwxr-xr-x 1 root wheel 1113 May 14 17:07 clear_fs_env.csh-rwxr-xr-x 1 root wheel 4458 May 14 17:07 compute_interrater_variability.csh-rwxr-xr-x 1 root wheel 4490 May 14 17:07 compute_label_volumes.csh-rwxr-xr-x 1 root wheel 214788 May 14 17:07 compute_vox2vox-rwxr-xr-x 1 root wheel 6389728 May 14 17:07 connectgraph-rwxr-xr-x 1 root wheel 6776500 May 14 17:07 conv1d_test-rwxr-xr-x 1 root wheel 7133948 May 14 17:07 conv1d_test_cuda-rwxr-xr-x 1 root wheel 6794716 May 14 17:07 convgaussian_test-rwxr-xr-x 1 root wheel 7119796 May 14 17:07 convgaussian_test_cuda-rwxr-xr-x 1 root wheel 1010 May 14 17:07 cor_to_minc-rwxr-xr-x 1 root wheel 4378 May 14 17:07 cp-dicom-rwxr-xr-x 1 root wheel 6893596 May 14 17:07 createMorph-rwxr-xr-x 1 root wheel 1851 May 14 17:07 cuda_setup-rwxr-xr-x 1 root wheel 76 May 14 17:07 cudadetect-rwxr-xr-x 1 root wheel 13308 May 14 17:07 cudadetect.bin-rwxr-xr-x 1 root wheel 12100 May 14 17:07 datastruct_utils.py-rwxr-xr-x 1 root wheel 6122 May 14 17:07 dcmdir-info-mgh-rwxr-xr-x 1 root wheel 23416 May 14 17:07 dcmunpack-rwxr-xr-x 1 root wheel 938 May 14 17:07 deface_subject-rwxr-xr-x 1 root wheel 8865 May 14 17:07 defect-seg-rwxr-xr-x 1 root wheel 4616 May 14 17:07 dicom-rename-rwxr-xr-x 1 root wheel 6452672 May 14 17:07 dmri_mergepaths-rwxr-xr-x 1 root wheel 6651560 May 14 17:07 dmri_paths-rwxr-xr-x 1 root wheel 6545252 May 14 17:07 dmri_pathstats-rwxr-xr-x 1 root wheel 6460264 May 14 17:07 dmri_spline-rwxr-xr-x 1 root wheel 6525716 May 14 17:07 dmri_tensoreig-rwxr-xr-x 1 root wheel 6660692 May 14 17:07 dmri_train-rwxr-xr-x 1 root wheel 6519924 May 14 17:07 dmri_trk2trk-rwxr-xr-x 1 root wheel 6501728 May 14 17:07 dmri_vox2vox-rwxr-xr-x 1 root wheel 6265 May 14 17:07 dmrirc.example-rwxr-xr-x 1 root wheel 7361 May 14 17:07 dmrirc.long.example-rwxr-xr-x 1 root wheel 20888 May 14 17:07 dsh-rwxr-xr-x 1 root wheel 14691 May 14 17:07 dt_recon-rwxr-xr-x 1 root wheel 31462 May 14 17:07 epidewarp.fsl-rwxr-xr-x 1 root wheel 6944772 May 14 17:07 exportGcam-rwxr-xr-x 1 root wheel 313 May 14 17:07 extract_talairach_avi_QA.awk-rwxr-xr-x 1 root wheel 8070 May 14 17:07 feat2segstats-rwxr-xr-x 1 root wheel 12563 May 14 17:07 feat2surf-rwxr-xr-x 1 root wheel 581 May 14 17:07 findsession-rwxr-xr-x 1 root wheel 756 May 14 17:07 fix_subject-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-lh-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-rh-rwxr-xr-x 1 root wheel 731 May 14 17:07 fix_subject_corrected-rwxr-xr-x 1 root wheel 1447 May 14 17:07 fix_subject_corrected-lh-rwxr-xr-x 1 root wheel 1358 May 14 17:07 fix_subject_corrected-rh-rwxr-xr-x 1 root wheel 952 May 14 17:07 fix_subject_on_seychelles-rwxr-xr-x 1 root wheel 3369 May 14 17:07 fixup_mni_paths-rwxr-xr-x 1 root wheel 5781 May 14 17:07 flip4fsl-rwxr-xr-x 1 root wheel 23072 May 14 17:07 flip_4dfp-rwxr-xr-x 1 root wheel 9859960 May 14 17:07 flirt.fsl-rw-r--r-- 1 root wheel 2919 May 14 17:07 flirt.newdefault.20080811.sch-rwxr-xr-x 1 root wheel 1408 May 14 17:07 fname2ext-rwxr-xr-x 1 root wheel 1438 May 14 17:07 fname2stem-rwxr-xr-x 1 root wheel 855 May 14 17:07 freesurfer-rwxr-xr-x 1 root wheel 184 May 14 17:07 freeview-rwxr-xr-x 1 root wheel 445424 May 14 17:07 fsPrintHelp-rwxr-xr-x 1 root wheel 4352 May 14 17:07 fs_lib_check-rwxr-xr-x 1 root wheel 635 May 14 17:07 fs_time-rwxr-xr-x 1 root wheel 7691 May 14 17:07 fscalc-rwxr-xr-x 1 root wheel 5794 May 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pctsurfcon-rwxr-xr-x 1 root wheel 2283 May 14 17:17 petsc_setup-rwxr-xr-x 1 root wheel 22465 May 14 17:17 plot_structure_stats.tcl-rwxr-xr-x 1 root wheel 4323 May 14 17:17 predict_v1.sh-rwxr-xr-x 1 root wheel 26812 May 14 17:17 progressbar.tcl-rwxr-xr-x 1 root wheel 259 May 14 17:17 qdec-rwxr-xr-x 1 root wheel 8733444 May 14 17:17 qdec.bin-rwxr-xr-x 1 root wheel 658640 May 14 17:17 qdec_glmfit-rwxr-xr-x 1 root wheel 1764 May 14 17:17 qt_setup-rwxr-xr-x 1 root wheel 209408 May 14 17:17 rbftest-rwxr-xr-x 1 root wheel 7611 May 14 17:17 rcbf-prep-rwxr-xr-x 1 root wheel 15908 May 14 17:17 rebuild_gca_atlas.csh-rwxr-xr-x 1 root wheel 268538 May 14 17:17 recon-all-rwxr-xr-x 1 root wheel 23095 May 14 17:17 recon-all.makefile-rwxr-xr-x 1 root wheel 22846 May 14 17:17 reg-feat2anat-rwxr-xr-x 1 root wheel 4341 May 14 17:17 reg-mni305.2mm-rwxr-xr-x 1 root wheel 6376400 May 14 17:17 regdat2xfm-rwxr-xr-x 1 root wheel 2503 May 14 17:17 register.csh-rwxr-xr-x 1 root wheel 972 May 14 17:17 register_child-rwxr-xr-x 1 root wheel 1106 May 14 17:17 register_elderly_subject-rwxr-xr-x 1 root wheel 971 May 14 17:17 register_subject-rwxr-xr-x 1 root wheel 967 May 14 17:17 register_subject_flash-rwxr-xr-x 1 root wheel 986 May 14 17:17 register_subject_mixed-rwxr-xr-x 1 root wheel 763 May 14 17:17 reinflate_subject-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-lh-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-rh-rwxr-xr-x 1 root wheel 993 May 14 17:17 remove_talairach-rwxr-xr-x 1 root wheel 763 May 14 17:17 renormalize_T1_subject-rwxr-xr-x 1 root wheel 788 May 14 17:17 renormalize_subject-rwxr-xr-x 1 root wheel 1002 May 14 17:17 renormalize_subject_keep_editting-rwxr-xr-x 1 root wheel 75392 May 14 17:17 repair_siemens_file-rwxr-xr-x 1 root wheel 948 May 14 17:17 reregister_subject_mixed-rwxr-xr-x 1 root wheel 9158 May 14 17:17 rtview-rwxr-xr-x 1 root wheel 6291 May 14 17:17 run-qdec-glm-rwxr-xr-x 1 root wheel 3732 May 14 17:17 run_mris_preproc-rwxr-xr-x 1 root wheel 1676 May 14 17:17 segment_monkey-rwxr-xr-x 1 root wheel 1443 May 14 17:17 segment_subject-rwxr-xr-x 1 root wheel 1732 May 14 17:17 segment_subject_notal-rwxr-xr-x 1 root wheel 1545 May 14 17:17 segment_subject_notal2-rwxr-xr-x 1 root wheel 1516 May 14 17:17 segment_subject_old_skull_strip-rwxr-xr-x 1 root wheel 1585 May 14 17:17 segment_subject_sc-rwxr-xr-x 1 root wheel 1599 May 14 17:17 segment_subject_talmgh-rwxr-xr-x 1 root wheel 3330 May 14 17:17 setlabelstat-rwxr-xr-x 1 root wheel 10224 May 14 17:17 sfa2fieldsign-rwxr-xr-x 1 root wheel 774 May 14 17:17 show_tal-rwxr-xr-x 1 root wheel 220 May 14 17:17 skip_long_make_checks-rwxr-xr-x 1 root wheel 8771600 May 14 17:17 slicetimer.fsl-rwxr-xr-x 1 root wheel 707 May 14 17:17 sphere_subject-rwxr-xr-x 1 root wheel 882 May 14 17:17 sphere_subject-lh-rwxr-xr-x 1 root wheel 881 May 14 17:17 sphere_subject-rh-rwxr-xr-x 1 root wheel 6558884 May 14 17:17 spherical_stats-rwxr-xr-x 1 root wheel 1802 May 14 17:17 spm_t_to_b-rwxr-xr-x 1 root wheel 5922 May 14 17:17 spmmat2register-rwxr-xr-x 1 root wheel 21612 May 14 17:17 spmregister-rwxr-xr-x 1 root wheel 2455 May 14 17:17 sratio-rwxr-xr-x 1 root wheel 6554748 May 14 17:17 stat_normalize-rwxr-xr-x 1 root wheel 1829 May 14 17:17 stem2fname-rwxr-xr-x 1 root wheel 8756 May 14 17:17 stim_polar-rwxr-xr-x 1 root wheel 556 May 14 17:17 subject_info.py-rwxr-xr-x 1 root wheel 10583672 May 14 17:17 surf2vol-rwxr-xr-x 1 root wheel 7698 May 14 17:17 surfreg-rwxr-xr-x 1 root wheel 1494 May 14 17:17 t4img_4dfp-rwxr-xr-x 1 root wheel 265468 May 14 17:17 t4imgs_4dfp-rwxr-xr-x 1 root wheel 1049 May 14 17:17 tal_QC_AZS-rwxr-xr-x 1 root wheel 856 May 14 17:17 tal_compare-rwxr-xr-x 1 root wheel 5185 May 14 17:17 talairach-rwxr-xr-x 1 root wheel 3115 May 14 17:17 talairach2-rwxr-xr-x 1 root wheel 6835816 May 14 17:17 talairach_afd-rwxr-xr-x 1 root wheel 5387 May 14 17:17 talairach_avi-rwxr-xr-x 1 root wheel 1132 May 14 17:17 talairach_mgh-rwxr-xr-x 1 root wheel 14605 May 14 17:17 talsegprob-rwxr-xr-x 1 root wheel 2405 May 14 17:17 tcl_setup-rwxr-xr-x 1 root wheel 10407 May 14 17:17 test_fs_tutorial.csh-rwxr-xr-x 1 root wheel 25884 May 14 17:17 test_recon-all.csh-rwxr-xr-x 1 root wheel 668968 May 14 17:17 tetgen-rwxr-xr-x 1 root wheel 3231 May 14 17:17 thickdiffmap-rwxr-xr-x 1 root wheel 102 May 14 17:17 tkmedit-rwxr-xr-x 1 root wheel 8859 May 14 17:17 tkmeditfv-rwxr-xr-x 1 root wheel 106 May 14 17:17 tkregister2-rwxr-xr-x 1 root wheel 6493700 May 14 17:17 tkregister2_cmdl-rwxr-xr-x 1 root wheel 103 May 14 17:17 tksurfer-rwxr-xr-x 1 root wheel 43553 May 14 17:17 trac-all-rwxr-xr-x 1 root wheel 26633 May 14 17:17 trac-paths-rwxr-xr-x 1 root wheel 58360 May 14 17:17 trac-preproc-rwxr-xr-x 1 root wheel 15106 May 14 17:17 tractstats2table-rwxr-xr-x 1 root wheel 75180 May 14 17:17 tridec-rwxr-xr-x 1 root wheel 110675 May 14 17:17 unpack_ima.tcl-rwxr-xr-x 1 root wheel 45265 May 14 17:17 unpack_ima1.tcl-rwxr-xr-x 1 root wheel 38901 May 14 17:17 unpack_mnc.tcl-rwxr-xr-x 1 root wheel 6596 May 14 17:17 unpackimadir-rwxr-xr-x 1 root wheel 35562 May 14 17:17 unpackimadir2-rwxr-xr-x 1 root wheel 18546 May 14 17:17 unpackmincdir-rwxr-xr-x 1 root wheel 145 May 14 17:17 unpacksdcmdir-rwxr-xr-x 1 root wheel 46836 May 14 17:17 unpacksdcmdir.tcl-rwxr-xr-x 1 root wheel 4690 May 14 17:17 usbtree-rwxr-xr-x 1 root wheel 3743 May 14 17:17 vno_match_check-rwxr-xr-x 1 root wheel 7108540 May 14 17:18 volume_copy_test_cuda-rwxr-xr-x 1 root wheel 4659 May 14 17:18 vsm-smooth-rwxr-xr-x 1 root wheel 3339 May 14 17:18 vtk_setup-rwxr-xr-x 1 root wheel 5376 May 14 17:18 wfilemask-rwxr-xr-x 1 root wheel 7046 May 14 17:18 wm-anat-snr-rwxr-xr-x 1 root wheel 2550 May 14 17:18 xfmrot-rwxr-xr-x 1 root wheel 9128 May 14 17:18 xhemireg-rwxr-xr-x 1 root wheel 445416 May 14 17:18 xmlToHtml-rwxr-xr-x 1 root wheel 5265 May 14 17:18 xsanatreg-rwxr-xr-x 1 root wheel 23032 May 14 17:18 zero_lt_4dfp ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found.Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download "unKnow" file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample2. put file in $FREESURFER/bin/4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command)5. start trac-all -prep6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano

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Yeo_JNeurophysiol11_FreeSurfer.zip
by Peter Savadjiev 07 Jun '13

07 Jun '13

Hello, I'm trying to download ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip (as linked from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011) however, the file doesn't seem to be available, or the server is not responsive. Is there another location from where I could download this file? Thank you, Peter

3 2

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