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30132 discussions

mri_nu_correct.mni
by Anna Josefson 11 Jul '13

11 Jul '13

Hi list, I have been trying to test out bias correction on hi-res post mortem animal MRI data. (which is not going through regular FS analysis pipeline) Is there any option for not changing the resolution ? from mri_nu_correct.mni.log: Original Data has (0.234375, 0.234375, 0.400003) mm size and (384, 384, 137) voxels. Data is conformed to 1 mm size and 256 voxels for all directions. Thanks a lot! Anna

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Fwd: Fwd: how to use mris_register?
by fatma zribi 11 Jul '13

11 Jul '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/7/10 Subject: Re: [Freesurfer] Fwd: how to use mris_register? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Copie1/s000_open_brain_sanlm_+TIR_normlalized$ ls -l total 704 drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 label drwxrwxr-x 4 zribi.f scalp 4096 Jul 5 17:12 mri drwxrwxr-x 2 zribi.f scalp 4096 Jul 9 10:44 scripts drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 SD drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 src drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 stats drwxrwxr-x 6 zribi.f scalp 4096 Jul 9 10:44 surf drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 tmp drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 touch drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 trash 2013/7/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > I meant can you run it and send us the results? If we can't open the file > it is not an FS issue, but something with the file system. Run ls -l with > the same path that you are giving mris_register > > > Bruce > > > On Wed, 10 Jul 2013, fatma zribi wrote: > > Hi Bruce, >> Yes i can run ls -l in the directory >> >> >> 2013/7/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Fatma >> >> are you sure you don't have a typo in the path? Can you run ls -l >> on that file? >> Bruce >> On Wed, 10 Jul 2013, fatma zribi wrote: >> >> >> >> ---------- Forwarded message ---------- >> From: fatma zribi <zribi.fatma(a)gmail.com> >> Date: 2013/7/10 >> Subject: Re: [Freesurfer] how to use mris_register? >> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >> >> Hi Bruce, >> >> Thank you very much for your help but it still don't work. >> >> mris_register s000_open_brain_sanlm_+TIR_** >> normlalized/surf/lh.sphere >> avg_all_subjects_SD/lh.reg.**template.tif lh.sphere_reg >> >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ >> reading surface from s000_open_brain_sanlm_+TIR_** >> normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_**sanlm_+TIR_normlalized/surf/**lh.sphere): >> could not open file >> No such file or directory >> mris_register: could not read surface file >> s000_open_brain_sanlm_+TIR_**normlalized/surf/lh.sphere >> No such file or directory >> >> note that the file exist in the folder and i have changed the >> SUBJECT_DIR to the appropriate folder >> >> Thank you very much for your help >> >> with best regards, >> >> Fatma >> >> >> >> 2013/7/9 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Fatma >> >> don't use the -1 flag if you are regtering to a >> template, only if you are registering individual >> surfaces to each >> other. You probably want the output to be named >> lh.sphere_reg and go in the s000/surf dir. >> >> cheers >> Bruce >> >> On Tue, 9 Jul 2013, fatma zribi wrote: >> >> Dear Mr, >> >> When I execute mris_register to register one >> subject to a template., I have this message of >> error: >> >> mris_register -1 s000/surf/lh.sphere >> avg_all_subjects_SD/lh.reg.**template.tif sphere_reg >> treating target as a single subject's surface... >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 >> nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 >> nicks Exp $ >> reading surface from s000_open_brain_sanlm_+TIR_* >> *normlalized/surf/lh.sphere... >> MRISread(s000_open_brain_** >> sanlm_+TIR_normlalized/surf/**lh.sphere): could not open file >> No such file or directory >> mris_register: could not read surface file >> s000/surf/lh.sphere >> No such file or directory >> >> note that the file exist in the specifeid >> SUBJECT_DIR >> >> Thank you for your help >> >> Fatma >> >> >> >> >> >> 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<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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polar angle and eccentricity with different parameters
by Bianca van Kemenade 11 Jul '13

11 Jul '13

Dear Freesurfers, When I only had 3 runs of polar angle data for retinotopic mapping, I used for example this command to make the analysis: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 12 -paradigm rtopy.par -fwhm 5 -fsd bold For some new subjects I have 3 runs of polar angle mapping and 3 runs of eccentricity mapping, with different parameters (cycle duration differs). Is it possible to analyse polar angle and eccentricity in one go? If so, what do I put under the -retinotopy flag? Thanks, Bianca -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/

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Reconstruction of the rat pial surface
by Shani Ben Amitay 11 Jul '13

11 Jul '13

Hello freesurfers I'm trying to reconstruct the pial and white surfaces of the rat. The input image is an inverted T2 (attached) and the segmentation to white and gray matter is done using an in house tool. using the following I'm trying to extract the surfaces: mri_fill -CV 120 128 89 -PV 124 137 111 -PV 123 133 113 -PV 123 136 110 -PV123 134 117 mri/white.mgz mri/filled/filled.mgz mri_pretess mri/filled/filled.mgz 255 mri/brain.mgz mri/filled-pretess255. mgz mri_tessellate mri/filled-pretess255.mgz 255 surf/lh.orig.nofix mris_extract_main_component surf/lh.orig.nofix surf/lh.orig.nofix mris_smooth -nw surf/lh.orig.nofix surf/lh.smoothwm.nofix mris_inflate -no-save-sulc surf/lh.smoothwm.nofix surf/lh.inflated.nofix mris_make_surfaces -noaparc -noaseg -mgz -T1 brain ratT1 lh -pial The white surface(red) is ok, the pial surface(yellow) not at all. Any idea if it's possible to fix it? is it possible to give the gray matter segmentation as an initial guess? Thanks ! Shani _______________________________________________ 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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Questions regarding QDEC
by jh kim 10 Jul '13

10 Jul '13

Dear FreeSurfer experts... Please be patient with a newbie's questions. For the first time, I'm trying to analyze between-group differences in cortical thickness (controls vs. patients) by using FS 5.1.0 and QDEC. I've read through the online manual and mailing lists; however, I cannot figure out the following queries. 1) I selected 'group' (con, pat) as a fixed factor (gender is not applicable because all are females), and demeaned age as a continuous covariate. After analyzing using DODS option, several questions are shown in the Display GUI panel. Does the question "Does the average thickness differ between con and pat?" mean between-group difference of cortical thickness after *controlling for the effect of age*? 2) Should I include average cortical thickness of the left or right cortex (calculated from the command, mris_anatomical_stats -l lh.cortex.label -f subid.txt subid lh) as a nuisance variable? I know this issue has been addressed many times before, and it is generally recommended not to include as a nuisance factor. However, in case of statistically significant difference in mean cortical thickness of one hemisphere (unpaired two sample t-test by SPSS), is it still not necessary to include it as a nuisance factor? From the similar points of view, how about volume and surface area analyses (include or not total cortical volume and total surface area as a nuisance factor, respectively) ? 3) I found several significant clusters that are corrected for multiple comparisons using Monte Carlo simulation (corrected P < 0.01) in the bottom of Display panel. I assume that this procedures take 10,000 permutations by default. Am I right? 4) Last question, how can I extract individual value (cortical thickness per subject) from the significant clusters? I want to do this 'all-at-once'. Please let me know the command. Apology for bothering you. Any comments would be greatly appreciated. Thanks. Kim

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freesurfer registration problem
by Lijia Wang 10 Jul '13

10 Jul '13

Hi experts, When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from BOLD images to the MNI305 template are always only a small part of the original images. I tried to use another T1_152 template instead(higher resolution) of the original MNI305 template, then"recon-all", "preproc-sess", but the results still remain the small part. How can I solve this problem? Thanks! Best Regards! Rebecca

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converting a volume to a surface
by Aaron Tanenbaum 10 Jul '13

10 Jul '13

Hola Freesurfers, I am new to Freesurfer and still learning the basics. I have been given a project and have not found a way to do it. Part of this task involves taking a 4dfp volume time series and convert it to a time series of a surface. This 4dfp I have is a statistical analysis mapped on to a specific atlas volume. Does anyone know of a way to do this. Any help will be highly appreciated. Gracias Aaron Tanenbaum

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Recon-all command not found
by Stéphane Poulin 10 Jul '13

10 Jul '13

Hello Freesurfer experts I have just installed Freesurfer and tried to run recon-all command. I get these "command not found" errors. Any idea? Stephane Last login: Wed Jul 10 21:42:55 on ttys001 [silicium:~] stephanep% cd /Volumes/Macintosh_HD_Donnees/Applications/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv FREESURFER_HOME freesurfer [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME freesurfer FSFAST_HOME freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR freesurfer/subjects MNI_DIR freesurfer/mni [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv SUBJECTS_DIR /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% recon-all -i /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm -subjid 002_S_4171 Subject Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects Actual FREESURFER_HOME /Volumes/Macintosh_HD_Donnees/Applications/freesurfer Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: freesurfer/bin/recon-all: No such file or directory /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171 \n mri_convert /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/mri/orig/001.mgz \n mri_convert: Command not found. Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s 002_S_4171 exited with ERRORS at Wed Jul 10 21:53:13 EDT 2013 For more details, see the log file /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep%

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Re: [Freesurfer] application of mri_cvs_register question
by Hoptman, Matthew 10 Jul '13

10 Jul '13

Hi Lilla, Unfortunately, when I run: mri_vol2vol --targ ../../../cvs_avg35_inMNI152/mri/norm.mgz --m3z ../../cvs/cvs_avg35_inMNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg diff2anat.bbr.mat --mov ../dtifit_FA.nii.gz --o diffvol2CVS.nii.gz --no-save-reg I now get: Using the m3z file as it is; no assumed location. regio_read_register(): Success Error reading R[3][0] from diff2anat.bbr.mat Matrix from regfile: -0.001 0.972 -0.234 -3.311; -0.001 0.234 0.972 69.949; 0.000 0.000 0.000 1.000; 0.000 0.000 0.000 0.000; Best, Matt -----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Wednesday, July 10, 2013 6:07 PM To: Hoptman, Matthew Subject: RE: [Freesurfer] application of mri_cvs_register question Hi Matt, As diff2anat.bbr.mat was created by bbregister, I believe you should be able to use --reg diff2anat.bbr.mat in your command. Let me know if you encounter further problems. Lilla On Wed, 10 Jul 2013, Hoptman, Matthew wrote: > Hi Lilla, > I want to apply the transform to both the dtifit_FA and tracula tracts to put them into cvs space (given the m3z file, as well). The goal is to get "average" tracts across my subjects. The relevant transforms I have in my dmri/xfms would seem to be: > diff2anat.bbr.mat > diff2anatorig.bbr.mat > diff2mni.bbr.mat > > Thanks, > Matt > -----Original Message----- > From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] > Sent: Tuesday, July 09, 2013 8:01 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] application of mri_cvs_register question > > > Hi, > > What type of registration file do you have representing the diff2anat > transformation? With mri_vol2vol you can use many different types of > transformations, if you switch the --reg flag to --xfm, --fsl or --lta, > for example. > > Lilla > > On Mon, 8 Jul 2013, Hoptman, Matthew wrote: > >> >> Hi all, >> >> I see how to apply mri_vol2vol to DTI data from dt_recon, but I’m not clear on how to do so to DTI data processed in Tracula. The command in the “Multimodal integration and inter-subject registration” tutorial is: >> >> mri_vol2vol --targ templateid --m3z morph.m3z --noDefM3zPath --reg 2anat.register.dat --mov diffvol --o diffvol2CVS --no-save-reg >> >> >> >> But in Tracula, there are no “register.dat” files, or indeed no *.dat files. Is there a way to convert one of the *.mat files in the dmri/xfms directory to a *.dat file? Also, given that I think Tracula and dt_recon use different transformation algorithms, which Tracula >> transform should I choose? >> >> >> >> Thanks, >> >> Matt >> >> >> >> Matthew J. Hoptman, PhD >> Research Scientist V >> Nathan S. Kline Institute for Psychiatric Research >> >> Research Associate Professor in Psychiatry >> NYU School of Medicine >> >> >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this >> e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. >> >> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> >> ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you >> are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, >> you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >> > > > 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. > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Discrepancy between surface data of Heschl's gyrus and its image
by Klein, Holger 10 Jul '13

10 Jul '13

Dear Freesurfers, I averaged 42 subjects with make_average_subject focusing on Heschl's Gyrus and finally got the image attached (for both atlases (Desikan = Atlas I, Destrieux = Atlas II). Gray matter surface calculations for Heschl's gyrus showed the following mean values (in mm^2): Atlas I lh = 439 (SD 60), rh = 323 (SD 46) Atlas II lh = 340 (SD 70), rh = 253 (SD 47) Heschl's gyrus depicted in the attached image looks considerably larger for Atlas II, but the surface analysis gives me smaller values for mean surface calculation (Atlas II < Atlas I) How can that be explained? Thanks in advance Holger

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