Freesurfer

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16 participants
30084 discussions

creating label for dlpfc
by Prapti Gautam 11 Feb '09

11 Feb '09

Dear all, I am trying to measure the volume of the dorsolateral prefrontal cortex in a large group of subjects. I have created a new label that only includes the dlpfc for a subject but realised that the same label file cannot be used on another subject. Has anyone created a customised ROI for dlpfc to use in a group of large subjects or can point me in the right direction ? The only other option I know is to individually create a label file for each subject which would be very time consuming. Thanking you in advance, Prapti

3 5

freeglut ERROR
by Lars M. Rimol 11 Feb '09

11 Feb '09

Hi, In tksurfer, when I have loaded an overlay and then try to add a color bar, I get this error message: freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glutInit' I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in freeglut (I think it's the latest version). Anyone know how to fix this? Thank you! -- yours, LMR

2 1

How to show only some parcellations
by Jürgen Hänggi 11 Feb '09

11 Feb '09

Dear FS experts Is there any possibility to show only some and not all of the parcellations of the lh.aparc.a2005s.annot annotation file? We have looked for in the archives but did not find any answer Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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. ----------------------------------------------------------------------------

3 2

Error message
by Jürgen Hänggi 11 Feb '09

11 Feb '09

Dear FS experts I tried to reconstruct the surface models of a patient's brain with large anomalies (see attachment). There is a large topological defect which FS cannot fix. FS failed with the following error message: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 169740 ambiguous faces found in tessellation segmenting defects... 87 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 10 into 0 -merging segment 26 into 0 -merging segment 61 into 3 -merging segment 39 into 31 -merging segment 0 into 36 -merging segment 45 into 37 -merging segment 53 into 37 -merging segment 56 into 37 -merging segment 64 into 54 -merging segment 69 into 66 -merging segment 72 into 70 76 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/altin_pre1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8502 (-4.4251) -vertex loglikelihood: -6.6049 (-3.3024) -normal dot loglikelihood: -3.5099 (-3.5099) -quad curv loglikelihood: -6.1072 (-3.0536) Total Loglikelihood : -25.0721 CORRECTING DEFECT 0 (vertices=29, convex hull=52) After retessellation of defect 0, euler #=-24 (121052,354507,233431) : difference with theory (-73) = -49 CORRECTING DEFECT 1 (vertices=27, convex hull=23) After retessellation of defect 1, euler #=-23 (121054,354521,233444) : difference with theory (-72) = -49 CORRECTING DEFECT 2 (vertices=48634, convex hull=6250) mris_fix_topology(4721) malloc: *** mmap(size=1417760768) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin Freesurfer.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Feb 11 00:01:09 CET 2009 [Freesurfer:/Applications/freesurfer/subjects] Nicki% Any suggestions? What does bus error mean? How does I can force FS to correct this large defect? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) 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. ----------------------------------------------------------------------------

2 1

scale factor in talairach transformations
by Cindy Eckart 10 Feb '09

10 Feb '09

Dear freesurfers, I am new in the list and will start with a hopefully not too stupid question... besides a planned cortical thickness analysis I would like to compare the volumes for some cortical parcellation areas between three groups. As far as I understood the freesurfer-procedures the brains are also stretched during the linear registration in the talairach transformation process. Is this stretching scale factor already accounted for in the volume values displayed in the aparc.statsvolume-file? Or will I have to account for potential deformations due to stretching of the brain by myself? I think it must have been already accounted for, but so far I found no specific notations in the corresponding publications... Thank you for your help and greetings from Germany Cindy ____________________________________________________________________ Psssst! Schon vom neuen WEB.DE MultiMessenger gehört? Der kann`s mit allen: http://www.produkte.web.de/messenger/?did=3123

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lGI value aberrantly too high but no topological defect
by Christian Scheel 10 Feb '09

10 Feb '09

Dear Marie, dear all, just to let you know: I have successfully overcome the problem by relaunching recon-all -hemi ?h -autorecon2 -autorecon3 for the brain in question. After the relaunch the lGI calculation worked perfectly and finished without errors. Best regards, Christian Scheel ### Dear Christian, I am aware that the lGI may occasionnally exit with the error you mentionned in some rare cases of pial surfaces with normal euler neumbers. I am working on debugging it. In the mean time, if this is only for one subject, is it possible for you to recreate the surfaces just for the hemisphere where you have this problem (i.e. relaunching recon-all -hemi ?h -autorecon2 and -autorecon3)? This would probably be the easiest way to overcome the aberrantly high lGI issue, as it will change very slightly the position and the total number of vertices of the white and pial surfaces, which will normally solve the problem. However, that implies that you would have to redo any statistical analyses that you may have already done on cortical thickness or cortical volumes (but there is no reason that the results would change just with reprocessing one hemisphere with the same freesurfer version). Let me know how it goes, Marie Quoting Christian Scheel <demi_...(a)gmx.net>: Dear all, I have successfully run 'recon-all -lgi' for all my subjects. However the computation process stopped in one of the brains claiming an lGI vertex value was aberrantly too high and giving me the following error message: ##### ... remeasuring lGI value for vertex iV = 32501. It may take a few minutes. WARNING -- Problem for vertex iV = 32501, lGI value is aberrantly high (lGI=40.5282)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/home/freesurfer/christian/34/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! ##### I have already restarted the computation twice without success. The script always crashes at the same vertex. The error message and the wiki page mention such an error in connection with possible topological defects. However when I check the mris_euler_number for the subject's rh.pial it interestingly does not show me any topological defect. Here is the output: ##### [freesur...@localhost ~/christian]$ mris_euler_number /home/freesurfer/christian/34/surf/rh.pial euler # = v-e+f = 2g-2: 133775 - 401319 + 267546 = 2 --> 0 holes F =2V-4: 267546 = 267550-4 (0) 2E=3F: 802638 = 802638 (0) total defect index = 0 ##### In all other brains the lGI calculation was successful. Does anyone of you have an idea? Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry -- Jetzt 1 Monat kostenlos! GMX FreeDSL - Telefonanschluss + DSL für nur 17,95 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a

1 0

mri_watershed error
by Kathy Zhang 09 Feb '09

09 Feb '09

Hello all, I've been working with a set of about 200 brains, and in 19 of these I'm getting the error "mri_watershed Error: GLOBAL region of the brain empty !". I've checked the talairach transformation with tkregister2, and in 17 of those cases, the transformations look fine (the two other cases were just bad scans). I'm using freesurfer version 4.0.5 for linux, and have already tried previous suggestions to run a skull strip off orig.mgz and checking the FOV values on T1.mgz and orig.mgz. Does anyone know what I could do to fix this error or somehow work around it to continue the skull strip? Thanks, Kathy Zhang

2 2

dt_recon
by Siddharth Srivastava 09 Feb '09

09 Feb '09

Hi everyone, I have recently started using the dt_recon processing pipeline in freesurfer. I just ran a dataset through it, and had a few questions about the methodology 1) How does the script calculate the mask from the DW data set. Is there any way to influence the mask calculation routine? I am familiar with bet/bet2 and i have an set of parameters tuned to my dataset. within dt_recon, i get the entire volume as a mask, while fsl generated a nice inclusive mask. Is there any way i can use the bet generated mask with dt_recon? 2) why is a glm fit done at the end of the processing stage? best regards, sid.

2 3

"preproc-sess" failing at 3dvolreg
by Krishna Srihasam 09 Feb '09

09 Feb '09

Hi, I am trying to analyze my fMRI data ( collected at MGH) using FSFAST and I was following the tutrial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastWorkFlows) I was able to unpack the data. But when I run "preproc-sess -s <subject_name> -fwhm 2", it fails at 3dvolreg. Here is the log file fmc.nii.mclog. I checked the tempvol.nii.gz . afni was able to open it and disply the slice. Any help is welcome. regards, krishna /tmp/sk/FSFAST/abe_090116/bold /usr/local/imports/freesurfer/fsfast/bin/mc-afni2 --i 005/f.nii --t 005/f.nii --frame 0 --o 005/fmc.nii --mcdat 005/fmc.mcdat Thu Jan 22 19:07:38 EST 2009 uid=2308(sk) gid=12308(sk) groups=11(floppy),17(audio),18(video),19(cdrom),12308(sk),12345(spm),12349(numbra) ives Linux ives 2.6.24.5-smp #2 SMP Wed Apr 30 13:41:38 CDT 2008 i686 Intel(R) Xeon(R) CPU E5405 @ 2.00GHz GenuineIntel GNU/Linux /usr/local/imports/freesurfer/bin/3dvolreg mcdat file is 005/fmc.mcdat tmp dir is 005/tmp.mc-afni2.15217 #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/tempvol.nii.gz --nskip 0 --ndrop 160 -odt float nskip = 0 ndrop = 160 $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... Dropping last 160 frames writing to 005/tmp.mc-afni2.15217/tempvol.nii.gz... #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float mri_convert 005/f.nii 005/tmp.mc-afni2.15217/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.34202, -0.939693) k_ras = (-0, -0.939693, 0.34202) changing data type from 4 to 3 (noscale = 0)... writing to 005/tmp.mc-afni2.15217/invol.nii.gz... #@# -------------------------------- /tmp/sk/FSFAST/abe_090116/bold 3dvolreg -verbose -dfile 005/fmc.mcdat -base 005/tmp.mc-afni2.15217/tempvol.nii.gz -prefix 005/tmp.mc-afni2.15217/outvol.nii.gz 005/tmp.mc-afni2.15217/invol.nii.gz ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ** ERROR (nifti_image_read): failed to find header file for '005/tmp.mc-afni2.15217/tempvol.nii.gz' ** Couldn't open -base dataset 005/tmp.mc-afni2.15217/tempvol.nii.gz ERROR: 3dvolreg

2 1

adding uncached variable to qdec
by Juranek, Jenifer 09 Feb '09

09 Feb '09

Hi, Running FSv4.2.0 on RHEL4. I'd like to add a variable such as lgi to qdec analyses. I created a .Qdecrc and .fsgd file, ran the lgi files through mris_preproc & mri_surf2surf (following instructions for Uncached Data posted under Group Analysis of the FsTutorial). While the output of mri_glmfit displays nicely in tksurfer, I'd like to look at the data within qdec (where scatter plots are easily viewed). The error I receive within qdec is as follows: <1st subject in fsgd file>/surf/?h.<var_name>.fwhm<smoothing factor>.fsaverage.mgh does not exist Is there an easy (e.g. scripted) way to generate the files within each subjects' /surf dir for a new variable not already recognized by the -qcache script for use by qdec? Many Thanks for any suggestions/solutions, Jenifer

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