Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

version
by Feng-Xian Yan 10 Dec '07

10 Dec '07

Hi, I want to use freesurfer to quantify cortical thickness, and I want to use the software under Linux fedora core 4. My computer's equipment is Quad-Core processor Intel Q6600, DDR2 memory 4GB, Sata2 disks 320G, GeFORCE8600. Which version do you recommend? i386? or x86_84? Thanks

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mri_convert problem while unpacking functionals
by Dan Dillon 10 Dec '07

10 Dec '07

Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1 localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3 T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: --------------------------------------------------------- Run 9 ----------------------------------------- Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz)

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conversion
by Anca-Larisa Sandu 10 Dec '07

10 Dec '07

I have a question about conversions. Is it possible to convert a file with the extension ".mgz" from Freesurfer to a file with the extension ".img", which can be read for example in SPM? If it is possible how should I do this conversion? Thank you in advance! Anca Sandu ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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tkmedit-sess error
by anisha narula 10 Dec '07

10 Dec '07

Hello, I am doing a retinotopy study, and when I view the slices using the sliceview-sess command I obtain activation in the regions desired. However, when I view results on the flattened patches, activation is messed up. I tried running the tkmedit-sess command. tkmedit-sess -analysis rtopy -contrast h -map t -sf sessid -df sessdir and it gave me this error: INFO: Found session in: /home/anisha87/freesurfer/subjects//ac1_ret grep: /home/anisha87/freesurfer/subjects//ac1_ret/session.info: No such file ordirectory INFO: Found session in: /home/anisha87/freesurfer/subjects//ac1_ret grep: /home/anisha87/freesurfer/subjects//ac1_ret/session.info: No such file ordirectory -------------------------------------------------------------- tkmedit-sess logfile is /home/anisha87/freesurfer/subjects/ac1_ret_study/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /home/anisha87/freesurfer/subjects INFO: subject is ac1_anatomical INFO: subject is ac1_anatomical ------------------------ SUBJECTS_DIR /home/anisha87/freesurfer/subjects /home/anisha87/freesurfer/subjects/ac1_ret_study tkmedit ac1_anatomical orig -overlay /home/anisha87/freesurfer/subjects/ac1_ret/bold/rtopy/eccen/h_000.bfloat -overlay-reg /home/anisha87/freesurfer/subjects/ac1_ret/bold/register.dat -fthresh 2 -fmid 5 -fslope 1 ------------------------ *corRead(): can't open file /home/anisha87/freesurfer/subjects/ac1_anatomical/mri/orig/COR-.info * * Error: Loading volume orig* Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. tkmedit failed The file located in.the direcotory orig is 001.mgz I can send it if needed. When I run tkmedit for MT localization study for the same subject, I get the same error. Thank You

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Surfaces, asegs, aparcs, Subcortical Structures
by James N. Porter 10 Dec '07

10 Dec '07

Hello FreeSurfer Folks- I've seen several threads in the archives discussing the expected inaccuracies in the pial, white, and orig surfaces running through subcortical structures. However, I've been unable to ascertain exactly how much and what kind of inaccuracy is acceptable. It makes sense to me that if the entirety of a structure, say the amygdala, were included or excluded in the pial surface, then it would be easy to adjust later measurements. However, what we see in all of our subjects is a random pattern of half in/half out, with weird shapes, when it comes to the surfaces running in and around subcortical structures. For example, take a look the image at this link. http://www.tc.umn.edu/~norb0062/Amygdala.tiff There you will see the how the hippocampus and amygdala are both half included in the pial surface. Item 1 has a strange guitar-shaped chunk taken out of the amygdala, and item 2 has a triangle and a peanut-shaped area removed. Are these the types of expected and accepted inaccuracies, or is there something afoul here that needs to be corrected? I have one other question regarding the interactions of aseg and surface information. Item 3 in the image points out a section of apparent subdural matter that has been classified as grey matter in the aseg but has been excluded from the pial surface. When the final statistics are spit out of recon-all, is there a section of processing that says something like, "Based on the aseg values my grey matter volume is X, but since Y of that is outside of the pial surface I'll call my total volume X-Y"? Or, is this another item to that requires correction and re-running of recon-all? Many thanks in advance, -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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surface problems around insula
by Michael Harms 10 Dec '07

10 Dec '07

Hello, We have observed several instances now where the surfaces around the insula are incorrectly constructed, with the pial surface being pulled inward toward the putamen. The likely source of this problem is that there is no obvious white matter between the putamen and insular cortex. Based on a previous suggestion, we tried editing the aseg to add a thin strip of putative white matter between the labels for the putamen and cortex, but this didn't prevent the problem. jpegs of the brainmask, aseg, and wm volumes are attached to illustrate. These data were processed using FS v4.0.1, EXCEPT that we used the most recent development version of mris_make_surfaces (v 1.105, built 11/2/2007) that we could find at the ftp site. Two questions: 1) Should we be concerned about fixing this type of pial surface problem in the insular cortex? (i.e., since this region typically seems to get labelled as 'unknown' in the aparc parcellation should we just ignore defects of this type?) 2) What controls the degree to which the ?h.white surfaces are allowed to deviate from the ?h.orig surfaces? In particular, while the orig surface is reasonable for this brain in the putamen/insular region (because it follows wm.mgz, which we can edit if need be), the putative white surface is too medial. The notes in 'recon-all' for the 'finalsurfs' stage state that "The white surface is created by "nudging" the orig surface so that it closely follows the white-gray intensity gradient as found in the T1 volume". How does one prevent the white surface from being "nudged" too far away from the orig surface, as occurred for this brain? thanks, Mike Harms -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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ROI labels for geometry vertices
by Sergey Plis 10 Dec '07

10 Dec '07

Hi, Please, help me to find out how to extract information I need. For each vertex in the geometry of the cortical surface I want an additional label that tells me which ROI this vertex belongs to. I extract all geometrical information using: mne_read_surfaces in matlab. This, however, does not give me the labels for ROI of each vertex. I plan to use freesurfer atlas for ROIs, but if anyone has a general answer that is suitable for any atlas I will be happy. A step by step guide would be appreciated :) Thanks! -- Sergey

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wmparc/white matter problems?
by Ryan Muetzel 08 Dec '07

08 Dec '07

Hello, We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions. Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)? Any help is much appreciated! -Ryan

2 4

mri_convert and VB15
by Jason Webster 07 Dec '07

07 Dec '07

Hello, After upgrading our scanner software to VB15A, we began receiving the following error from mri_convert when running unpacksdcmdir: ERROR: incorreclty formatted version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B15 Maj = -1073750848, Min=-1073771672, MinMin = -1208005856 child process exited abnormally ERROR: mri_convert The error seems to be arising from the parsing of the software version in the DICOM metadata; below are pre and post versions of the relevant line: Software Version : syngo MR B13 4VB13A Software Version : syngo MR B15 >From what I have been told, this is the official version and the metadata from the MGH scanner is the same. Has anyone else encountered this? We are currently using the unpacksdcmdir and mri_convert from v3.0.5 - are there other versions of these that will read DICOMs from VB15? Thanks, Jason

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buglet in fast_inorm
by Sebastian Moeller 07 Dec '07

07 Dec '07

Dear fellow freesurfers, using FreeSurfer 3.0.5 and 4.0.1, I can make fast_inorm.m (as called by inorm) die, with otherwise innocently looking inputs. The syndrom is that if my fist slice contains only one iunder voxel twf_under (see 3.0.5's line 88 of fast_inorm.m) is initialised as scalar (that is not an array), any subsequent try to store a n_timepoint long vector in twf_under just makes matlab choke. This same combination of input dimensionality is fixed for twf_over in the same code. Applying the same special casing of single voxels for iunder solves my problems for good. Here is the meat of the change: if(nthslice,1) > 0) twf_under(nthslice,:) = mean(y2(iunder,:)); else with the following construct: if(nunder(nthslice,1) > 1) twf_under(nthslice, 1) = mean(y2(iunder,:)); elseif (nunder(nthslice,1) == 1) twf_under(nthslice, 1) = y2(iunder,:); else Ahoi & thanks supplying powerful tools Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Freesurfer December 2007