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30132 discussions

Error with mri_glmfit-sim
by Antonella Kis 28 Sep '11

28 Sep '11

Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in this case so I can get as output my cortical thickness values for the formed clusters at threshold 2, before multiple comparison? Many thanks, AK

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analysis.cfg not generated by mkanalysis-sess
by Po-Jang (Brown) Hsieh 28 Sep '11

28 Sep '11

Dear all, I ran mkanalysis-sess (mkanalysis-sess -analysis junk -TR 2 -paradigm para01.para -event-related -funcstem fmc -nconditions 3 -runlistfile runlist_odd -fsd bold -fir 10 30 -native) but it did't not generate analysis.cfg. The only file I can see after running this is analysis.info. When I ran mkanalysis-sess.new, both analysis-info and analysis.cfg are generated as fine. Could any one know how to solve this problem? ps. I'm running freesurfer5.1.0 on Mac OS X 10.6.8 (the mkanalysis-sess.new is a copy from freesurfer4.5.0). Thanks! Brown

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correction
by Oertel, Viola 28 Sep '11

28 Sep '11

Dear Freesurfers, could you please give me detailed information about the Bonferroni or clusterwise correction we can do in Freesurfer? How much iterations? Is that cluster- oder voxelwise? Is there anywhere a detailed description about the correction options? Best regards, Viola

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fieldsign-sess: ERROR Surf/src mismatch
by Michelle Umali 28 Sep '11

28 Sep '11

Dear Freesurfers, This is related to my retinotopy analysis tksurfer-sess dimension mismatch error message. So another subject had these errors come up during fieldsign-sess selxavg3-sess -a rtopy.self.lh -s sjXX -force (which ran without error) then I ran fieldsign fieldsign-sess -a rtopy.self.lh -occip -s sjXX and got: ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. What may have caused this? Thanks. Michelle

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aparc.annot question from August
by Keefe, Helen L 28 Sep '11

28 Sep '11

Hi Everyone, I have not received a response on this question from August -= cold we revisit it please? thanks, Helen [Freesurfer] Saving annotation and stats after expand boundary of region Keefe, Helen L helen-keefe at uiowa.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Saving%20annotation%20and%20stats%20after%20expand%20boundary%20of%0A%09region&In-Reply-To=%3C353409BC97D32F48B41827FF380DD9A105F2DC%40hc-mailboxc1-n4.healthcare.uiowa.edu%3E> Tue Aug 16 12:10:25 EDT 2011 * Previous message: [Freesurfer] update v5.1 and trac-all command <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019884.h…> * Next message: [Freesurfer] Abnormal segmentation of hippocampal subfields <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019832.h…> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/date.htm…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/thread.h…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/subject.…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/author.h…> ________________________________ Hi Bruce, Doug, and All, I have corrected a boundary between lh corpuscallosum and caudalanteriorcingulate. I have overwritten the label/lh.aparc.annot as per Bruce's email below. However, doesn't this leave a number of files with incorrect information now in the stats directory? Do I need to rerun something to bring these up to date? Thanks, Helen ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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Retinotopy tksurfer-sess: ERROR: mask and surf dimensions don't match
by Michelle Umali 27 Sep '11

27 Sep '11

Hi Doug and Freesurfers I didn't change any of the structural After the retinotopy analysis. First, I ran recon-all -all. Second, I made edits to to brainmask.mgz and wm.mgz and then ran autorecon2-wm and autorecon3. Third, I cut the occipital patches in tksurfer and then flattened them. Finally, after all of this, I ran the retinotopy analysis (please see below) on the functional images. Where would the dimsension mismatch of the mask and surf occur in this pipeline? How does one overcome this? I would really be very grateful for any assistance. Thanks very much. Michelle ________________________ TERMINAL OUTPUT Here are the analysis commands I used the error output for viewing the map is below it : mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj07 -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sj07 -force selxavg3-sess -a rtopy.self.rh -s sj07 -force fieldsign-sess -a rtopy.self.lh -occip -s sj07 fieldsign-sess -a rtopy.self.rh -occip -s sj07 This is the output when I tried to view in tksurfer-sess BOTANICA:/usr/local/freesurfer/subjects/retinotopy> tksurfer-sess -a rtopy.self.lh -s sj07 -map angle Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Tue Sep 27 06:37:33 EDT 2011 /usr/local/freesurfer/bin/tksurfer list eccen polar con/map eccen /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz con/map polar /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz maplist /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz mri_concat /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz --o /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii cd /usr/local/freesurfer/subjects/retinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer ld07 lh inflated -overlay /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 -mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz -mask-thresh 2 -fthresh .01 Contrasts 0 eccen 1 polar setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 mrismaskfile /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 2.0000 setting fthresh to 0.0100 subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/retinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=156145, faces=312286 tkmedit: Trying to open /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii as registered functional volume. surfer: curvature read: min=-3.127128 max=2.364444 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8162 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(ld07) Reading mris mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz ERROR: dimension mismatch between mask and surf

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Error -FSGD file for clinical correlations please help
by Rajagopalan, Venkateswaran 27 Sep '11

27 Sep '11

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file "ERROR message: is no subjects specified" what am I doing wrong here , also my design matrix contrast is 1 0 am I right. I am interested in seeing whether there any correlation between cortical thickness changes in ALS patients with their ALSFRS score. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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recommended WM lesion filling procedure?
by Mishkin Derakhshan 27 Sep '11

27 Sep '11

Hi, I have a bunch of scans from patients with mulitple sclerosis. Since they all have substantial t2w hyperintensities I would like to automate the process of WM filling and re-running. Looking through the emails and the wiki, however, I am a bit confused. http://www.freesurfer.net/fswiki/FsTutorial/ControlPoints says I should NOT use control points for white matter lesions: "Control points should NOT be used to try and normalize a brain lesion to 110. Such defects should be fixed with white matter edits" BUT, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes says I should: "mris_make_surfaces: where wm lesions exist, even if the lesion is filled in wm.mgz volume, when mris_make_surfaces is run to create the final surfaces, because it uses brain.finalsurfs.mgz for its intensity info, and doesnt consider the fill data in wm.mgz, its possible for surfaces to not follow grey matter on the perimeter of the lesion. A fix will appear in a future release. A potential work-around is to set lesion voxels in brainmask.mgz and norm.mgz to 110 and lesions voxels in aseg.mgz to 77 (lesion mask can be derived manually or from an automated algorithm), then run recon-all -autorecon2-cp." I'm assuming that the guidance in the release notes supersedes the other wiki page but I wanted to make sure. thanks, mishkin

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QDEC stats table output
by Antonella Kis 27 Sep '11

27 Sep '11

Hi, After running QDEC, I would like to output in a table the thickness values within each clusters. I know this is a dependent variable and I can see the values on the plot but is there a way that I can get this values in a table? Thanks, Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: carolina.mr <carolina.mr(a)uol.com.br>; David Kennedy <dave(a)nmr.mgh.harvard.edu>; freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, September 23, 2011 11:38 AM Subject: Re: [Freesurfer] QDEC results and stats The "value" is the dependent variable (eg, thickness). doug Bruce Fischl wrote: > Hi Carolina > > I'll leave the 2nd question for Doug and Nick. The first one, I think > you mean "ventral DC", which is short for "ventral diencephalon". It's > a grab bag of a bunch of stuff that we can't resolve. You would need > to check with someone like Dave Kennedy (ccd) to get the exact > description. > > cheers > Bruce > > On Fri, 23 Sep 2011, carolina.mr wrote: > >> >> Hello, all, >> >> I have 2 questions: >> >> - Does anybody know which structure is represented or correspond to >> "left ventral IDC" in aseg segmentation? >> >> - In QDEC analysis, when we obtatin the significant clusters and see >> the linear regression or correlation curve, what does it mean the >> "value" of the curve? Is it the regression coeficient? The level of >> correlation? How shall I describe it? >> >> Thank you, Carolina >> >> >> > ------------------------------------------------------------------------ > > _______________________________________________ > 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: 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 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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retinotopy analysis: tksurfer-sess dimension error between mask and surf
by Michelle Umali 27 Sep '11

27 Sep '11

Dear Freesurfers, I am working on a retinotopy analysis and I got this error: ERROR: dimension mismatch between mask and surf when trying to look at map angle in tksurfer-sess Do I need to add --reshape flag? If so, where? Any help would be most appreciated. Thanks. Michelle Here are the analysis commands I used the error output for viewing the map is below it : mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj07 -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sj07 -force selxavg3-sess -a rtopy.self.rh -s sj07 -force fieldsign-sess -a rtopy.self.lh -occip -s sj07 fieldsign-sess -a rtopy.self.rh -occip -s sj07 This is the output when I tried to view in tksurfer-sess BOTANICA:/usr/local/freesurfer/subjects/retinotopy> tksurfer-sess -a rtopy.self.lh -s sj07 -map angle Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux Tue Sep 27 06:37:33 EDT 2011 /usr/local/freesurfer/bin/tksurfer list eccen polar con/map eccen /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz con/map polar /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz maplist /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz mri_concat /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz --o /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii cd /usr/local/freesurfer/subjects/retinotopy setenv SUBJECTS_DIR /usr/local/freesurfer/subjects tksurfer ld07 lh inflated -overlay /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 -mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz -mask-thresh 2 -fthresh .01 Contrasts 0 eccen 1 polar setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 mrismaskfile /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz... setting mrismaskthresh to 2.0000 setting fthresh to 0.0100 subject is ld07 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/retinotopy checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/ld07) Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/ld07/mri/orig.mgz surfer: vertices=156145, faces=312286 tkmedit: Trying to open /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.dat surfer: Interpreting overlay volume /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii as registered functional volume. surfer: curvature read: min=-3.127128 max=2.364444 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 8162 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(ld07) Reading mris mask /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz ERROR: dimension mismatch between mask and surf

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