Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

[freesurfer] recon-all taking an unusually very long time
by David Qixiang Chen 15 Dec '09

15 Dec '09

Hi, We are having one scan going through recon-all that is taking way longer than ordinary. Other scans took about 20-30 hours to calculate, while this particular scan is taking 3+ days and has still not being completed. Just wondering how often something like this happens, and if there's any known problems with this sort of thing. Here's the mri_info output: Starting DICOMRead2() dcmfile = /media/HIPPO/scans/normals/C11/T1/C11_0.dcm dcmdir = /media/HIPPO/scans/normals/C11/T1 Ref Series No = 3 Found 162 files, checking for dicoms Found 160 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 160 ndcmfiles = 160 PE Dir = ROW (dicom read) Volume information for C11_0.dcm type: dicom dimensions: 256 x 256 x 160 voxel sizes: 0.9375, 0.9375, 1.0000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -80.0, zend: 80.0 TR: 11.96 msec, TE: 5.05 msec, TI: 300.00 msec, flip angle: 20.00 degrees nframes: 1 ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = -0.0000, c_r = 5.3850 : x_a = 0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 30.3850 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 27.4266 Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -0.9375 0.0000 -0.0000 125.3850 0.0000 -0.9375 -0.0000 150.3850 0.0000 0.0000 1.0000 -52.5734 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.878906 ras to voxel transform: -1.0667 0.0000 0.0000 133.7440 0.0000 -1.0667 0.0000 160.4107 -0.0000 -0.0000 1.0000 52.5734 0.0000 0.0000 0.0000 1.0000

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Mris_make_face_parcellation
by Jürgen Hänggi 15 Dec '09

15 Dec '09

Dear FS experts When using mris_make_face_parcellation is it possible to restrict the face parcellation to a parcellation found in aparc.a2005s, e.g. to the precentral gyrus. Or is there another way to decide which micro-parcellation produced by mris_make_face_parcellation belong to which parcellation in aparc.a2005s? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Stats from cluster labels
by Dankner, Nathan (NIH/NIMH) [F] 15 Dec '09

15 Dec '09

Hi all, I was curious as to whether I would be able to pull stats (i.e. Average cortical thickness) from a cluster after cluster correction. Is this possible, and if so, how would I go about doing it? Thanks, Nathan

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QDEC error
by Weisinger, Brian (NIH/OD) [E] 15 Dec '09

15 Dec '09

I am trying to use qdec but it gave me this error. I don’t understand what is wrong because it read the diagnosis factor level of COS & NV but then says subject 00308 has invalid level of COS in diagnosis column. Any ideas? CHP-MP2:freesurfer brianweisinger$ qdec & [1] 7902 CHP-MP2:freesurfer brianweisinger$ Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 24 Reading discrete factor levels from config file /Applications/freesurfer/subjects/qdec/gender.levels 'Female','Male', done Reading discrete factor levels from config file /Applications/freesurfer/subjects/qdec/diagnosis.levels 'COS','NV', done ERROR: Subject 00308 has an invalid level 'COS' in the diagnosis column INFO: If 'diagnosis' is a discrete factor, then create a file named 'diagnosis.levels' containing the valid factor names one per line. Error loading the data table.

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Strange occipital dip
by Bahadur, Kandy (NIH/NIMH) [F] 15 Dec '09

15 Dec '09

Hello, I am very new to freesurfer and might not have seen enough surfaces to know the answer to this question. But, I went through autorecon1 and autorecon2 with my volumes, and when I looked at the surface to inspect it, I found a weird , relatively large dip around the parietal and occiptal lobes. We are only interested in occipital (we cut that plane out and flatten it), so I am concerned that this dip might interfere with the data. When I looked at that point in the editor, nothing weird or abnormal showed up. I have attached a picture of the RH, where I see this abnormal dip. Can you let me know if this is normal or not? Also, the freesurfer manual nicely illustrates where I need to make the cuts to cut out the occipital lobe for the left hemisphere, but I don't really see any guidelines for cutting out the occipital lobe for the right hemisphere. Any suggestions? Thanks, Kandy -- Kandy Anasha Bahadur National Institute of Mental Health/ National Institute of Health Laboratory of Brain and Cognition 10 Center Drive, Building 10/4C212 Bethesda, MD 20892 Phone: 301-435-4945 Email: bahadurk(a)mail.nih.gov

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Error mri_label2vo
by Ribes Delphine 15 Dec '09

15 Dec '09

Hi FreeSurfer users, I've tried the following from my $SUBJECT_DIR/SubjectX/mri directory: mri_label2vol --seg aseg.mgz --regheader rawavg.mgz --o aseg-in-rawavg.mgz --temp aseg.mgz I have the following error in return: ERROR: Option --regheader unknown Any ideas where does it comes? Thanks a lot, Have a good day, Delphine ________________________________________ De : Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Date d'envoi : mardi 3 novembre 2009 18:48 À : Ribes Delphine Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Re: [Freesurfer] RE : RE : Skull Stripping Free surfer Check out this page and see if it answers your questions https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Ribes Delphine wrote: > Hi, > > I've tested to use directly mri_watershed but then you have to set the seeds for watershed initiaization. > > The idea is to create an automatic pipeline (as I have a bunch of data to process) and get the results into the subject space coordinate. > > In subjects directories, I've seen one called transform. Inside this directory, there is some file with (I suppose) the affine transform applied. Is there a freeSurfer command to do the inverse transform? > Also there is a "conformalization" to put all volume in 256 cube with 1mm cube spacing. Is there a command in FreeSurfer to get back the original volume? > > After the inverse affine transform and the inverse conformalization, I will have (hopefully), my skullstrip volume into his original space coordinate? > > Thanks > Delphine > > > > De : Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Date d'envoi : mardi 3 novembre 2009 15:09 > À : Ribes Delphine > Cc : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] RE : Skull Stripping Free surfer > > yes, it's possible. You'll need to download and install freesurfer, then > try out the mri_watershed command (or just run recon-all on your data, > mri_watershed is one of the steps it runs) > On Tue, 3 Nov 2009, Ribes > Delphine wrote: > > >> Hi, >> >> Looking at Literature, HWA algorithm seems to perform well for my kind of data. Also the results I've got seems to confirm this hypothesis. But if possible I would like to siwcth of the affine registration. >> >> So yes I would like only to do skull strip using HWA algorithm. Is it possible to do so in freesurfer? :-) >> >> Thanks >> >> ________________________________________ >> De : Pedro Paulo de Magalhães Oliveira Junior [ppj(a)netfilter.com.br] >> Date d'envoi : mardi 3 novembre 2009 13:43 >> À : Ribes Delphine >> Cc : freesurfer(a)nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Skull Stripping Free surfer >> >> Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :) >> >> Are you sure you just want to skull strip? >> >> >> 2009/11/3 Ribes Delphine <delphine.ribes(a)epfl.ch<mailto:delphine.ribes@epfl.ch>> >> Dear Users, >> >> I've just started using FreeSurfer. I would like to use it for skull-stripping. >> >> I've created a batch file to process all my subjects. >> and I am basically using the command line: >> >> recon-all -autorecon1 -skullstrip -s subj1 >> >> I would like to know if there is a way to only do skull-stripping and not doing the Talairach Transform and then INU correction? >> >> I would like to have the skulll-stripp volume in the same space coordinate as originally? >> >> Otherwise, I am doing skull-stripping of T1 weighted images of normal elderly subejcts. Is there any specific recommandation for skull-stripping parameters? >> >> Thanks a lot, >> Delphine >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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 >> >> >> >> > > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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qdec output
by Guang Zeng 15 Dec '09

15 Dec '09

Hi, there, Does anyone can give me link or paper which explains all the QDEC output file, such as F.mgh, gamma.mgh, beta.mgh ....... What are they, how are they related? Thanks a lot! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/171222985/direct/01/

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pediatric template vv. scaling or parcellation?
by Rhoshel Lenroot 14 Dec '09

14 Dec '09

Hello - We are planning to use freesurfer in a study of 2-5year olds; I understand from previous posts that image intensity should be ok at this age range, but was wondering whether there are issues related to scaling or parcellation such that it would still be optimal to use a pediatric template? Thank you very much, Rhoshel Lenroot, M.D. School of Psychiatry University of New South Wales r.lenroot(a)unsw.edu.au

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SetUp file error
by Ilana Hairston 14 Dec '09

14 Dec '09

Hi there, I moved my data to a new computer with Freesurfer installed. When i run the SetUpFreeSurfer.csh (or .sh for that matter) i get a strange configuration: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/ FSFAST_HOME /usr/local/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer//subjects MNI_DIR /usr/local/freesurfer//mni FSL_DIR /usr/local/fsl note the double slashes on SUBJECTS_DIR, FSFAST_DIR, and MNI_DIR. needless to say freesurfer can't find my data. I inspected the setup files and they don't have typo in them. what should i do? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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Re: [Freesurfer] func2roi-sess bug?
by John Richey 14 Dec '09

14 Dec '09

Ok - I believe I figured out the problem, but I wanted to post it to the list, so that anyone else who encounters this error can hopefully spend less time than I did tracking down the culprit! Essentially, a break was being passed inappropriately to the mri_vol2roi subroutine called by func2roi-sess. The break (return/enter, etc) was located in the .txt file that specified the run numbers that I wanted to analyze (in my case, 007 008 009). These strings were separated by a space and a break, which caused the srcvol to equal srcvol = bold/007 /fmcsm8 And this caused func2roi-sess to terminate with errors when it couldn't find such a file. -----Original Message----- From: John Richey Sent: Friday, December 11, 2009 4:30 PM To: 'Freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] func2roi-sess bug? I am using v4.5.0, on CentOS 5.4. Here is the log: [jar62@meehl freesurfer]$ func2roi-sess -roidef l_lingual -analysis dotprobe_all_hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig.nii -sf subjectlist.txt -d /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer/ ---------------------------------------------------------- func2roi-sess logfile is /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/log/func2ro i-sess.log ---------------------------------------------------------- ----------------------------------------------------- Session: SAD_C17 1/26 Fri Dec 11 16:05:23 EST 2009 Fri Dec 11 16:05:23 EST 2009 --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h roitxtfile = bold/dotprobe_all_hrf/l_lingual/h.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h.nii ...done INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) INFO: Readjusting Frame Power --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h-offset roitxtfile = bold/dotprobe_all_hrf/l_lingual/h-offset.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h-offset.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h-offset.nii ...done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) 009ist: 007 ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 ------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007 [jar62@meehl freesurfer]$ mri_modify Usage: mri_modify <-xras xr xa xs> <-yras yr ya ys> <-zras zr za zs> <-cras cr ca cs> \ <-xsize size> <-ysize size> <-zsize size> \ <-tr recoverytime> <-te echotime> <-ti inversiontime> <-fa angledegree> \ <-xform new_file_name> \ involume outvolume [jar62@meehl freesurfer]$ func2roi-sess -roidef l_lingual -analysis dotprobe_all_hrf -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail pos -maskmap sig.nii -sf subjectlist.txt -d /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer/ -rawstem fmcsm8 -rawrlf dotprobe.txt ---------------------------------------------------------- func2roi-sess logfile is /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/log/func2ro i-sess.log ---------------------------------------------------------- ----------------------------------------------------- Session: SAD_C17 1/26 Fri Dec 11 16:57:34 EST 2009 Fri Dec 11 16:57:34 EST 2009 --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h --roiavg bold/dotprobe_all_hrf/l_lingual/h --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h roitxtfile = bold/dotprobe_all_hrf/l_lingual/h.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h.nii ...done INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) INFO: Readjusting Frame Power --------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcvol bold/dotprobe_all_hrf/h-offset --roiavg bold/dotprobe_all_hrf/l_lingual/h-offset --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/h-offset.txt version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/h-offset roitxtfile = bold/dotprobe_all_hrf/l_lingual/h-offset.txt oldtxtstyle = 0 srcvol = bold/dotprobe_all_hrf/h-offset.nii srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 srcreg Dsrc ------------- 0.999 -0.001 -0.043 -6.051; 0.036 -0.523 0.852 -10.837; 0.024 0.852 0.522 1.743; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -0.320 0.000 0.000 32.000; -0.000 -0.000 -0.320 32.000; -0.000 0.227 -0.000 16.000; 0.000 0.000 0.000 1.000; ---------------------------------- Reading bold/dotprobe_all_hrf//AllvFix/sig.nii NOT INVERTING Loading volume bold/dotprobe_all_hrf/h-offset.nii ...done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 1142 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 93 hits in final mask label2mask_linear: done Lxyz2Scrs: -0.320 0.000 0.014 33.936; -0.008 -0.273 -0.167 31.442; 0.008 -0.119 0.194 13.537; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 3673 label hits voxsize = 42.9687, rszthresh = 1e-07, thresh = 4.29687e-06 INFO: label2mask_linear: there were 277 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 93 Done averging over ROI (nhits = 93) 009ist: 007 ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 ------------------------------------------- -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C17 mri_vol2roi --srcreg bold/register.dat --label /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label --mskvol bold/dotprobe_all_hrf//AllvFix/sig.nii --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ -------------------------------------------------------- roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 oldtxtstyle = 0 /fmcsm8= bold/007 srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C17/lab el/lh.lingual.label labelreg unspecified label fill thresh = 1e-07 mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii mskfmt unspecified msk volume same as source msk tail = pos msk threshold = 0.000000 msk invert = 0 msk frame = 0 /fmcsm8. Does it exist?lume bold/007 that is bizarre. What version of freesurfer and what operating system are you using? doug John Richey wrote: > Dear freesurfer experts: > > I am trying to extract roi from my fMRI data using func2roi-sess. > However, I encounter an error that I wonder might be a bug in the > code? My input is func2roi-sess -roidef l_lingual -analysis hrf > -anatlabel lh.lingual -maskcontrast AllvFix -maskthresh 0 -masktail > pos -maskmap sig -sf subjects.txt > > (the last 25 or so lines of the log are pasted below). Basically, I > believe that line in the log that reads: > > /fmcsm8= bold/007 > > should read: > > srcvol = bold/007/fmcsm8.nii > > The result is that the func2roi-sess routine terminates with the error > displayed on the last line: /fmcsm8. Does it exist?lume bold/007 > > Has anyone else encountered this problem? Or maybe I am skipping a > step? I am using v4.5.0. If it helps, I can also paste my source > code that seems to produce this error. Thanks in advance > > John Richey > > > -------------------------------------------------------- > /mnt/users/jar62/hill/data/Dichter/DotPro.01/Analysis/freesurfer/SAD_C > 17 > mri_vol2roi > --srcreg bold/register.dat --label > /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C > 17/lab el/lh.lingual.label --mskvol > bold/dotprobe_all_hrf//AllvFix/sig.nii > --msksamesrc --mskthresh 0 --msktail pos --mskframe 0 --finalmskvol > bold/dotprobe_all_hrf/l_lingual/mask --roiavgtxt > bold/dotprobe_all_hrf/l_lingual/fmcs.txt07 > version $Id: mri_vol2roi.c,v 1.26.2.2 2008/04/02 22:28:56 greve Exp $ > -------------------------------------------------------- > roifile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 > .txtxtfile = bold/dotprobe_all_hrf/l_lingual/fmcsm8-007 > oldtxtstyle = 0 > /fmcsm8= bold/007 > srcfmt = bvolume > srcreg = bold/register.dat > srcregold = 0 > srcwarp unspecified > label file = > /home/jar62/net/hill/data/Dichter/DotPro.01/Analysis/freesurfer//SAD_C > 17/lab > el/lh.lingual.label > labelreg unspecified > label fill thresh = 1e-07 > mskvol = bold/dotprobe_all_hrf//AllvFix/sig.nii > mskfmt unspecified > msk volume same as source > msk tail = pos > msk threshold = 0.000000 > msk invert = 0 > msk frame = 0 > /fmcsm8. Does it exist?lume bold/007 > _______________________________________________ > 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 gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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