Re: [Freesurfer] \nu_estimate_np_and_em\ error during recon-all
Thanks Nick and Anil! I tried with the Bert data set in its original location, and got a different kind of error: ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I am now trying to run recon-all through FMRIB (FSL)... Tudor On 18 February 2013 00:25, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Thanks Anil! Tudor, sounds like you should give this a try. I'm re-posting this to the freesurfer list to archive it. Nick Hi I am having the same problem but I have an idea where it's occurring. I have Windows XP Virtualbox Ubuntu Install where I have an windows share on the Linux using shared folder from windows When I use the shared folder it gives this error When I use the Bert data set in its original location subjects dir it works fine When I transfer a new subject in virtualuser Freesurfer subjects folder it's works fine I ran it with -debug command to check and I thinks nu_ estimate makes some temp folders which gets messed up when you use shared folders. So to avoid this error transfer the subjects folder to virtualuser subject folder rather than using -sd command to specify a shared folder Sincerely Anil 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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] tkmedit error
Hello I'm new to freesurfer, I have some .nii images that i converted to .mgz via mri_converter in freesurfer and run recon-all on them! it seems everything is fine and i've got stats in m subjects folders. but when I try to do tkmedit to visualize images it gives me an error: 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. what should I do now?! thanks ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have done
would introduce
them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have
see NaNs for the following labels
1006 1033 2006 2013 2033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am having some
trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can be fixed).
Question: Is there any alternative to getting this correlation
matrix?
i.e every ROI against every other ROI?
Thanks,
S
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Re: [Freesurfer] Merging .annot files using mris_label2annot puts labels in the wrong place
Hi Chris, in the color table file, do you have an unkown entryas the first entry? There should be one or else use --no-unknown. doug On 02/16/2013 11:07 PM, Chris McNorgan wrote: Hi all, I posted this back in January, and got a direct email reply from someone on the mailing list, who gave me a helpful tip, but it doesn't seem to be working out quite right. The problem: I have 3 .annot files per hemisphere, each based on the ?h.aparc.annot files (36 regions), but in each file, a different subset of these 36 regions has been further subdivided using the connectomemapper toolkit. I would like to merge all the subdivided regions, the definitions of which are spread across 3 files, into a single .annot file for each hemisphere. The one response I received said: After running cmtk on a subject you'll notice that in /FREESURFER/labels there are folders for each parcellation called regenerated_?h_500 for example that contain all of the subdivided labels from that resolution Lausanne parcellation. I used mris_label2annot (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_label2annot) to combine all of the desired labels into a single annot. The trick is that you need to type each label name one at a time with an --l flag (easy to make a script to do this quickly) and you need to supply a clut file, which has to be in the format freesurfer is expecting (which is also easy to generate, and the colors can be arbitrary). I've been trying this for a few days now without success. I also tried deconstructing the original .annot files using mri_annotation2label and then reassembling the label files using mris_label2annot (in the event that the label files I had been previously using were somehow mangled). Either approach seems to land me in the same place. The regions are generally in the right general anatomical area, but most are out of place within those regions. For example I've got renderings comparing the original definition of precentral_1 (highlighted region in purple in ORIGINAL.tiff), which has become precentral_20 (in REDONE.tiff). Similarly, parsoparcularis_10 has become parsoparcularis_1. But parahippocampal_1 was found in the paracentral region. All of these shifts look as though the label came from an adjacent region (alphabetically, as my ctab and scripts list the regions alphabetically). Also notable is that the left has 500 entries in the ctab file, but running my script gives the following output: ...snip 499 8697855 transversetemporal_3 500 8763647 transversetemporal_4 501 -1 NOT_FOUND Mapping unhit to unknown Found 1526 unhit vertices Similarly, the script for the right side also tries to map 503/502 entries. These errors and the fact that the reassignments look like they are off-by-one errors leads me to suspect that it might have something to do with my ctab files, as the region boundaries seem to be maintained. If anyone has any suggestions, I'm going to include links to the renderings, my scripts that execute mris_label2annot for each hemisphere, and my ctab files. I'm hoping I've left enough clues for someone to see where I'm going wrong. Thanks, Chris I've linked 7 files to this email: ORIGINAL.tiff http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D(1.0 MB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/1ABD5WZOw65wPj3NK2M69D REDONE.tiff http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L(1.0 MB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/2PGqBjqUXCJl5RffOUkE3L lausanne_left.sh http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP(16.0 KB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/2PBnWtBTjXLCpVqxz7dgEP lausanne_right.sh http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM(16.1 KB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/3uag3ZBIhRNisK2sB8MrhM lh.lausanne_annot.ctab.csv http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU(17.0 KB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU rh.lausanne_annot.ctab.csv http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg(18.2 KB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/49H8V1gj7Ucq9FlIr8Onwg lh.lausanne_annot.ctab.csv http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU(17.0 KB)Ubuntu One https://one.ubuntu.com/referrals/referee/2149434/?next=/http://ubuntuone.com/2PFJrAqBtLSxU3yqPpdpjU Mozilla Thunderbird http://www.getthunderbird.com makes it easy to share large files over email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs:
Re: [Freesurfer] mri_label2vol: Brodmann Areas
You will have to merge the labels into an annotation (mris_label2annot),
then the annotation to a segmentation volume (mri_aparc2aseg), then
apply mri_label2vol to the segmentation.
doug
On 02/19/2013 10:45 AM, Vincent Koppelmans wrote:
Hi all,
I am trying to convert Brodmann area 4a and 4p to .nii file format in
native space. I have used to following syntax:
tkregister2 --mov ${SUBJECTS_DIR}/mri/rawavg.mgz --noedit --s
[SUBJECT_ID] --regheader --reg ./register.dat
mri_label2vol --label [PATH-TO-LABEL-FILE] --temp
${SUBJECTS_DIR}/mri/rawavg.mgz --subject [SUBJECT_ID] --hemi lh --o
[OUTPUT-FILE-NAME] --proj frac 0 1 .1 --fillthresh .0 --reg
[PATH-TO-register.dat-FILE]
This is the result: https://dl.dropbox.com/u/6747155/BA4a.png
As you can see, there are 'missing' voxels in the volume: it is not
one smooth shape. However, when I convert aseg or aparc structures to
volumes, I don't have this problem. Is it possible to get a a smooth,
fully filled shape from a Brodmann label?
Thanks in advance,
Vincent
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Re: [Freesurfer] selxavg3-sess illconditioned error
Hi katie, I'm guessing that you have one event type that only has one
event? If so, you can do what Sebastian suggests, but you won't be able
to look at contrasts related to that condition.
doug
On 02/19/2013 03:24 PM, Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS 4.5) where it is
giving me an Ill-conditioned error that I can't trace out.
I have 8 runs that I am running separately (same basic analysis for
each run, but each run gets it's own analysis for svm purposes).
Originally for this subject, I created an analysis and it ran fine
for all 8 runs. I went back and changed the timewindow on the
analysis (and only the timewindow) and now, while it runs fine for 7
or the 8 runs, one of them gives me an ill conditioned error during
selxavg3-sess. I double checked the paradigm file and all conditions
are listed, and the only change between when the analysis ran fine and
when it gave me this error was changing the timewindow. The
mkanalysis commands I used both times are listed below.
Original analysis (worked fine):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor
-runlistfile nodist_run${r}.txt -inorm -tpexclude tpexclude.dat
-nconditions 3 -timewindow 22 -TER 2 -noautostimdur -polyfit 2
end
new analysis (illconditioned on one run only):
foreach r (1 2 3 4 5 6 7 8)
mkanalysis-sess -analysis grating_nodist_ld_34_run${r} -TR 2 -paradigm
grating.dat -designtype event-related -funcstem fmc -motioncor
-runlistfile nodist_run${r}.txt -inorm -tpexclude tpexclude.dat
-nconditions 3 -timewindow 34 -TER 2 -noautostimdur -polyfit 2
end
Katie
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Re: [Freesurfer] Generate mask from surface in diffusion space
Hi Shani, it looks like your commands are right. How are you judging that the mask is thicker? What is the resolution of the DTI volume? When you binarize in a coarser space, you'll naturally not get it to line up with the surface, and the binary mask will naturally be thicker. doug On 02/21/2013 08:22 AM, Shani Ben Amitay wrote: Dear freesurfers I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated surfaces. for example to generate surface normals I used the following: mri_surf2surf --s subjectid --hemi lh --sval-nxyz white_surface_in_diffusion --tval lhwhitediffusion_n.mgh mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg mri/register.dat --outvol lh_white_n.img --template lowb.img Any idea what am I doing wrong? Thanks! Shani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_vol2vol call problem
Hi Greg, the target (--targ) should be a volume, not the name of a subject (eg, 816/mri/orig.mgz) doug On 02/21/2013 02:23 PM, Gregory Kirk wrote: Greetings lords of freesurfer! I am having a problem getting a combined cvs warp+bbregister to map an FA volume onto a template. mri_vol2vol --targ 816 --m3z combined_to816_elreg_afteraseg-norm.m3z --noDefM3zPath --reg /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat --mov /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz --o test --no-save-reg spits out Using the m3z file as it is; no assumed location. movvol /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/dtifit_FA.nii.gz targvol 816 outvol test regfile /study5/aa-scratch/TEENEMO/twins_tracula/recons/821/dmri/xfms/anatorig2diff.bbr.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1362252270 corRead(): can't open file /study5/aa-scratch/TEENEMO/twins_freesurfer/816/COR-.info i know i have not seen a file COR-.info in the top level subject directory in the modern age of the universe. i know i saw this before but my notes from the last time i figured this out got lost in a file system cleanup. can one of you tell me where i went astray ? thank you Greg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mgh conversion
Hi Glen, I think there is some confusion here about what this conversion is doing and what you want it to do. This conversion simply changes the way the information is stored, but it is still surface data. SPM/MRIcron cannot display surface data even if it is in nifti format. It sounds like what you want to to transform the surface data into volume data. For that you should use mri_surf2vol. doug On 02/21/2013 05:17 PM, Glen Lee wrote: Hi Doug, Just to re-assure your message below as I'm having the same issue, I've converted an mgh file with a total of 163,842 vertices into a nifti file using . And it reshapes the structure to 3D as shown below. fname: 'test_via_mr_conv.nii' dim: [27307 1 6] mat: [4x4 double] pinfo: [3x1 double] dt: [16 0] n: [1 1] descrip: 'FreeSurfer May 25 2011' private: [1x1 nifti] The fact that I'm not able to display the nifti file in SPM or MRIcron means that the conversion to Nifti doesn't work correct? - Glen On Mon, Jan 28, 2013 at 2:09 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: How many vertices are on the surface? For nifti you have to reshape the size of the image so that it fits in the nifti format (requires each dim be less than 32k). If the number of vertices has a prime factor that is more than 32k, then you cannot convert it to nifti and use it in another software package (it still works in FreeSurfer, but then you could just use an mgh file then). doug On 01/28/2013 01:58 PM, Courtney Haswell wrote: Hi, Was there a resolution to this thread on the FreeSurfer mail archive? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17886.html I am having the same issue trying to convert a cortical thickness sig.mgh to a NIfTI file. I want to use the statistically significant area as an ROI in another analysis. Thanks, Courtney Haswell -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] obtaining residuals after regressing out nuisance parameters
Hi Caspar, youcan do it that way and then extract the average time course from the residuals. Otherwise, you'd have to do the regression yourself in matlab. doug On 02/22/2013 11:01 AM, Caspar M. Schwiedrzik wrote: hm, I just realized that I should probably run selxavg3-sess with -svres and then take the residuals from the res folder, right? caspar 2013/2/22 Caspar M. Schwiedrzik cschwie...@rockefeller.edu: Dear Freesurfer experts, I am running some functional connectivity analyses using FSFAST in Freesurfer 5.1. I would like to compare seed time courses (which I later use as predictors) obtained after regular pre-processing with seed time courses obtained after regressing out several nuisance parameters. I am a little bit unsure how to use the output from selxavg3-sess for the latter. After defining a single subject analysis with mkanalysis-sess with -notask and only the nuisanance regressors (-nuisreg), I currently run selxavg3-sess with -no-con-ok and -run-wise. Can I then take the time courses from the respective beta.nii per run? Or am I completely off here? Thanks! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Hippocampus volume calculations
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote: Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4. I compare volumes (the same apply for lh and for rh) when calculating as: Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure. I obtain quite different values, for example: row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918 Am I doing anything wrong? Should I calculate the hippos subfields volumes differently? Many thanks! Gari ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Change of thickness with age with tksurfer
Hi Sophie, in the output directory there should be several folders, one for each contrast. One of those contrasts will be your age-slope contrast. Load the gamma.mgh file to see what the slopes are. doug On 02/25/2013 08:42 AM, Sophie Maingault wrote: Hello, I used qdec to visualize correlation between cortical thickness and age. With tksurfer, when I load the file sig.mgh I can see the p-value for each vertex (log10 pvalue) but I would like to load a file which show the value of the slope, I mean the change of thickness with age. Which file I have to use as overlay or how can I do it? Thanks a lot! Sophie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] creating figures using f-score color scale
Hi Maria, I don't know exactly how they generated it. It might not even have been using the FS tools. If I were to do it in FS, I would create a segmentation by thresholding the continuous map into the ranges of F values I wanted. I would then create an annotation (mris_seg2annot) where I can control the RGB color that each segmentation gets. make sense? doug On 02/24/2013 05:57 PM, Maria Jalbrzikowski wrote: Dear Freesurfer experts, I was wondering if you could help me in figuring out how to create a figure in tksurfer. A recent publication in PLoS One on William's Syndrome showed a figure with a color scale for the F-scores and reflected the F-values through colors that they obtained in ROI analyses. Does anyone have any suggestions for how they created this figure? I wrote the authors of the manuscript, but have not yet heard back. I would like to make a similar figure for some analyses I've recently run. I've attached a picture of the figure and the title of the article is Regional Brain Differences in Cortical Thickness, Surface Area and Subcortical Volume in Individuals with Williams Syndrome by Shashwath A. Meda, Jennifer R. Pryweller, Tricia A. Thornton-Wells Thank you for your help! Best, Maria Jalbrzikowski -- Maria Jalbrzikowski, M.A. University of California, Los Angeles ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] question mris_preproc
If there are negative values in the lh.area, then something is very wrong. Can you double check? If they persist, can you upload the subject? doug On 02/20/2013 10:18 AM, j janssen wrote: Hi, freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 $Id: mris_preproc,v 1.66 2012/12/06 16:06:17 mreuter Exp $ after recon-all i ran recon-all -s $subject -qcache this generates lh.area.fsaverage.mgh which only contains values 0 and higher while negative values exist for the lh.area of the same subject. is this normal and if so, why? thanks, -joost ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Recon-all with my own template
The first cmd (mris_register, or use the surfreg script) will create a new registration file in subject/surf. Make sure you don't overwrite the original one (?h.sphere.reg). mris_preproc will just create a single output file with all of your subjects' thickness data (unless you use --qcache) doug On 02/18/2013 05:58 AM, Sophie Maingault wrote: Hello, Thank you for your answer. I found this page : http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates So I have to do the point “Creating a registration template initialized with FreeSurfer template (DG)” : first the command mris-register –curv and then mris_preproc –surfreg ? But what type of file it will create ? In the directory surf ? It will change the parcellation ? Cheers Sophie *De :*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *De la p**art de*Douglas Greve *Envoyé :* vendredi 15 février 2013 18:02 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Recon-all with my own template You can also register your subjects to the new average subject (creates a new spherical registragtion). Use the surfreg script (run with --help for more info). doug On 2/15/13 8:55 AM, Bruce Fischl wrote: Hi Sophie what template do you mean? You can't rerun the subcortical segs or parcellations since they depend on manual labelings. You could regenerate our cortical folding patterns atlas, but I don't think that buys you much since the atlas you would build is by definition in register with our current one (if it wasn't you wouldn't be able to use our cortical parcellations) cheers Bruce On Fri, 15 Feb 2013, Sophie Maingault wrote: Hello Freesurfer experts ! I created a new template with make_average_subject called 80tvs and I would like to re-run some of my subjects with this new template. I can?t find the command line in FAQ. Is it for example : recon-all ?all ?s t0001 ?target 80tvs ?? So I need the repertory of this new template in the subject_dir ? Thank you for the answer ! Sophie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled out the correlation values (using the matlab code
below) after the automated registration process: regfeat2anat aseg2feat,
some ROIS reported NaNs.
When I manually checked the registration and adjusted it using tkregister2, I
found myself stretching/scaling to make it fit. Consequently I do not have
NaNs BUT I am now realising that I should'nt have to scale.
1) How can I check if left-right reversals have happened - its not obvious by
eye
2) I am going to re-run the automated registration and I can send you a pic
and the cost function..
Thanks,
S
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 10:44 AM
To: Bruce Fischl
Cc: Sudhin A. Shah
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
Stretching the registration? You should not need to stretch the reg.Are
you 100% positive that the func and anat come from the same subject and
there have been on left-right reversals? What is the final value of the
cost function?
doug
On 02/25/2013 10:06 AM, Bruce Fischl wrote:
Hi Sudhin
Doug would have some. You definitely shouldn't have to stretch/scale
to get it to fit. If you do, something critical is wrong. Also, please
cc the list so that the right person (Doug in this case!) can answer.
cheers
Bruce
On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
Hi Bruce,
They were a result of the registration (between structural and
functional) being 'off'. When I manually correct this using
tkregister2, they were fine. However, I found that I had to stretch
(scale) to get them to fit so (i started a new thread regarding this)
are there image examples on what this should look like so I can use
as a guide?
Thanks,
S
On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have
done would introduce them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL
(reg-feat2anat aseg2feat)
When I extract the values (as per the matlab code below), I see
NaNs in certain regions. Of the 19 datasets that I have analyzed I
have
see NaNs for the following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it
in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am
having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by
freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can
be fixed).
Question: Is there any alternative to getting this
correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the
Re: [Freesurfer] extracting hand drawn ROIs to Afni space
Hi Paul, do you still have a problem that needs to be solved? doug On 02/18/2013 04:39 PM, Paul Beach wrote: Thank you for forwarding this. I realize I need to further clarify my issue as well. With the help of Doug Greve I've taken hand made ROIs in tksurfer, repackaged them into a new annotation, and repackaged that into a new aseg file for an average subject. Now (and this is where I'm stuck) I'm trying to take those newly minted ROIs, place them onto individual subjects' brains and THEN send them to Afni for each of those subjects (before doing seed correlation analysis). Previously I had been using mri_label2label to place the averaged subject ROI into single subjects' folders and then mri_label2vol to get them ready to send to Afni. However, this method was not producing ROIs that covered the extent of a region's gray matter. Thus, Doug's solution of re-annotating and re-segmenting. Hopefully that makes things a bit easier. Thanks again for your help! Paul On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Paul we usually call those labels and have an ascii label file format. Not sure how to get that into AFNI, but I'm zure Ziad (ccd) knows. cheers Bruce On Mon, 18 Feb 2013, Paul Beach wrote: Hi there, Through the help of the Freesurfer QA staff I've been able to get ROIs drawn in tksurfer into an augmented aparc+aseg file of an averaged subject. I need to be able to get those ROIs, which are not part of the color LUT, into Afni space. For ROIs that are already in the LUT, getting them to Afni is no problem, I simply use a 3dcalc command. However, I have the problem of needing to export newly parcellated and segmented ROIs that aren't in the Freesurfer LUT to Afni space. Is there a way to do this short of creating a new spot for them in our LUT? If not, how does one go about adding ROIs to the LUT and/or creating a LUT specific to my needs (since the Wiki suggests not fussing with the original LUT)? Thanks, Paul -- 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. -- Paul Beach DO/PhD candidate - Year V Michigan State University - College of Osteopathic Medicine - OMS V - Neuroscience Program - Bozoki Lab: Neurology/Radiology - President: American Physician Scientist Association, MSU COM Chapter ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
0 0 0 1
round
Or in anat2exf.register.dat.mincost
0.545185 785.020257 804.709380 1.199352
This looks ok under manual inspection - although the head was not in an ideal
position (patient data). However, I cannot extract data from ROI label 2013.
Thanks,
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 11:39 AM
To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled out the correlation values (using the matlab code
below) after the automated registration process: regfeat2anat aseg2feat,
some ROIS reported NaNs.
When I manually checked the registration and adjusted it using tkregister2, I
found myself stretching/scaling to make it fit. Consequently I do not have
NaNs BUT I am now realising that I should'nt have to scale.
1) How can I check if left-right reversals have happened - its not obvious by
eye
2) I am going to re-run the automated registration and I can send you a pic
and the cost function..
Thanks,
S
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 10:44 AM
To: Bruce Fischl
Cc: Sudhin A. Shah
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
Stretching the registration? You should not need to stretch the reg.Are
you 100% positive that the func and anat come from the same subject and
there have been on left-right reversals? What is the final value of the
cost function?
doug
On 02/25/2013 10:06 AM, Bruce Fischl wrote:
Hi Sudhin
Doug would have some. You definitely shouldn't have to stretch/scale
to get it to fit. If you do, something critical is wrong. Also, please
cc the list so that the right person (Doug in this case!) can answer.
cheers
Bruce
On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
Hi Bruce,
They were a result of the registration (between structural and
functional) being 'off'. When I manually correct this using
tkregister2, they were fine. However, I found that I had to stretch
(scale) to get them to fit so (i started a new thread regarding this)
are there image examples on what this should look like so I can use
as a guide?
Thanks,
S
On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have
done would introduce them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL
(reg-feat2anat aseg2feat)
When I extract the values (as per the matlab code below), I see
NaNs in certain regions. Of the 19 datasets that I have analyzed I
have
see NaNs for the following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it
in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am
having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by
freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can
be fixed).
Question: Is there any alternative to getting this
correlation matrix?
i.e every ROI against every other ROI?
Thanks,
S
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
The cost (from .mincost) looks fine. Can you send a pic of the
registration inaccuracy?
doug
On 02/25/2013 11:53 AM, Sudhin A. Shah wrote:
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
0 0 0 1
round
Or in anat2exf.register.dat.mincost
0.545185 785.020257 804.709380 1.199352
This looks ok under manual inspection - although the head was not in an ideal
position (patient data). However, I cannot extract data from ROI label 2013.
Thanks,
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 11:39 AM
To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled out the correlation values (using the matlab code
below) after the automated registration process: regfeat2anat aseg2feat,
some ROIS reported NaNs.
When I manually checked the registration and adjusted it using tkregister2,
I found myself stretching/scaling to make it fit. Consequently I do not have
NaNs BUT I am now realising that I should'nt have to scale.
1) How can I check if left-right reversals have happened - its not obvious
by eye
2) I am going to re-run the automated registration and I can send you a pic
and the cost function..
Thanks,
S
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 10:44 AM
To: Bruce Fischl
Cc: Sudhin A. Shah
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
Stretching the registration? You should not need to stretch the reg.Are
you 100% positive that the func and anat come from the same subject and
there have been on left-right reversals? What is the final value of the
cost function?
doug
On 02/25/2013 10:06 AM, Bruce Fischl wrote:
Hi Sudhin
Doug would have some. You definitely shouldn't have to stretch/scale
to get it to fit. If you do, something critical is wrong. Also, please
cc the list so that the right person (Doug in this case!) can answer.
cheers
Bruce
On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
Hi Bruce,
They were a result of the registration (between structural and
functional) being 'off'. When I manually correct this using
tkregister2, they were fine. However, I found that I had to stretch
(scale) to get them to fit so (i started a new thread regarding this)
are there image examples on what this should look like so I can use
as a guide?
Thanks,
S
On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have
done would introduce them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL
(reg-feat2anat aseg2feat)
When I extract the values (as per the matlab code below), I see
NaNs in certain regions. Of the 19 datasets that I have analyzed I
have
see NaNs for the following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it
in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked perfectly 2 years ago :), but now I am
having some trouble.
I run reg-feat2anat aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by
freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.
Now I get an error (working with AFNI to see if it can
be fixed).
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
It does not look bad to me. Why do you think it looks wrong?
On 02/25/2013 12:29 PM, Sudhin A. Shah wrote:
Hi Doug,
Here's an example view... It looks fine to me. See attached..
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 12:12 PM
To: Sudhin A. Shah
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
The cost (from .mincost) looks fine. Can you send a pic of the
registration inaccuracy?
doug
On 02/25/2013 11:53 AM, Sudhin A. Shah wrote:
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
0 0 0 1
round
Or in anat2exf.register.dat.mincost
0.545185 785.020257 804.709380 1.199352
This looks ok under manual inspection - although the head was not in an
ideal position (patient data). However, I cannot extract data from ROI label
2013.
Thanks,
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 11:39 AM
To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled out the correlation values (using the matlab code
below) after the automated registration process: regfeat2anat aseg2feat,
some ROIS reported NaNs.
When I manually checked the registration and adjusted it using tkregister2,
I found myself stretching/scaling to make it fit. Consequently I do not
have NaNs BUT I am now realising that I should'nt have to scale.
1) How can I check if left-right reversals have happened - its not obvious
by eye
2) I am going to re-run the automated registration and I can send you a pic
and the cost function..
Thanks,
S
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 25, 2013 10:44 AM
To: Bruce Fischl
Cc: Sudhin A. Shah
Subject: Re: [Freesurfer] Registration segmentation with FSL -
obtaining correlation matrix..
Hi Sudhin, I'm not sure what the problem is. NaNs in the data?
Stretching the registration? You should not need to stretch the reg.Are
you 100% positive that the func and anat come from the same subject and
there have been on left-right reversals? What is the final value of the
cost function?
doug
On 02/25/2013 10:06 AM, Bruce Fischl wrote:
Hi Sudhin
Doug would have some. You definitely shouldn't have to stretch/scale
to get it to fit. If you do, something critical is wrong. Also, please
cc the list so that the right person (Doug in this case!) can answer.
cheers
Bruce
On Mon, 25 Feb 2013, Sudhin A. Shah wrote:
Hi Bruce,
They were a result of the registration (between structural and
functional) being 'off'. When I manually correct this using
tkregister2, they were fine. However, I found that I had to stretch
(scale) to get them to fit so (i started a new thread regarding this)
are there image examples on what this should look like so I can use
as a guide?
Thanks,
S
On Feb 25, 2013, at 9:27 AM, Bruce Fischl wrote:
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have
done would introduce them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with the rsfMRI via FSL
(reg-feat2anat aseg2feat)
When I extract the values (as per the matlab code below), I see
NaNs in certain regions. Of the 19 datasets that I have analyzed I
have
see NaNs for the following labels
10061033200620132033
Is this a known problem? Is there a solution?
Thanks,
S
On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:
Sorry, I don't think we have such a program. You could do it
in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
ind = find(a.vol == seglist(nthseg));
roimean(:,nthseg) = mean(fmat(:,ind),2);
end
m = roimean'*roimean;
On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:
Hello,
This worked
Re: [Freesurfer] Mac mountain lion installation problem
Paula, what is the processor type and speed? how much memory do you have on your system? Nick On Mon, 2013-02-25 at 11:50 +0100, Vieweg, Paula /DZNE wrote: Hi, I have installed Freesurfer (Leopard version) on Mac Mountain Lion and tried to use it for a full segmentation (recon-all -all). On my own files I get a problem with Talairach, the program aborts and I get the recommendation to try it with -notal–check. I have done this and Freesurfer has since then taken 6 days to run one brain. I have started the example script with Bert and it has run 4 days. I have aborted all the processes now and am asking for help. All other steps in the Testing protocol with Bert seem to work apart from the recon-all -all. I am using 7T data (but with just 1mm isotropic resolution), which is where I thought the problem came from. Since the example script also does not run (that is, does not finish), it seems to be a problem with the installation and possibly my Mac version. Do you have any suggestion how to solve this? Best, Paula Paula Vieweg Aging Cognition Research Group German Center for Neurodegenerative Diseases (DZNE) Building 15, Room 309a Leipziger Str. 44 39120 Magdeburg GERMANY phone: +49-391-67-24520 email: paula.vie...@dzne.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Remove medial wall label from surface?
Dear all, I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces? Thank you very much, Andries van der Leij ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FreeSurfer recon-all two sets of error
Recon is still running. I started the process on 2/21/2013. Its been 4 days. I ran this command, and viewed the aseg file, and that looks reasonable tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg Currently it is at this stage: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 124766 ambiguous faces found in tessellation segmenting defects... .. 61 defects to be corrected 0 vertices coincident .. .. CORRECTING DEFECT 31 (vertices=244, convex hull=142) After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory (-27) = -21 CORRECTING DEFECT 32 (vertices=44865, convex hull=8969) On Fri, Feb 22, 2013 at 5:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: I don't think either one of these are errors, just warnings that occur pretty frequently and I don't think should impact the results. Does the recon finish? Do the results look ok? On Fri, 22 Feb 2013, Blessy M wrote: I am getting the bottom two sets of errors while doing a simple recon-all. More specifically while running this command: recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 -autorecon3 Has someone encountered this kind of errors? Is there a fix? 1) Computing MAP estimate using 2772 samples... ** IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 7296.5 tol 0.10 ... ... 2) unfolding failed - restoring original position 0146: dt=13.779160, rms=0.814 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.814, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101542.133 ms iter 0, gcam-neg = 801 .. unfolding failed - restoring original position 0158: dt=13.828393, rms=0.814 (-0.069%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.814, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100610.148 ms 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/**compliancelinehttp://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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans
I'd collect highres T1w as well and then refine the 1mm surfaces using that. Peace, Matt. From: SHAHIN NASR sha...@nmr.mgh.harvard.edu Date: Monday, February 25, 2013 1:39 PM To: Freesurfer freesurfer@nmr.mgh.harvard.edu, Bruce Fischl fis...@nmr.mgh.harvard.edu, Doug Greve gr...@nmr.mgh.harvard.edu Subject: [Freesurfer] High resolution fMRI and resolution of anatomical scans Hi, We are planning to collect high resolution functional MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed anatomical scans with 1 mm voxel size. The question is, do we need to re-collect anatomical scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans
You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans
We always collect a low resolution whole brain mprage structural scan before the functional scans to help us position our slices. Can I use that? You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans
yes On 02/25/2013 03:23 PM, sha...@nmr.mgh.harvard.edu wrote: We always collect a low resolution whole brain mprage structural scan before the functional scans to help us position our slices. Can I use that? You do not need another one unless you think that the brain has changed in some way between when you collected the anat and the func. Also, if you are going to acquire a partial field of view (ie, only part of the brain), make sure you get a full brain acq of something to help in registration (--int flag with BBR). This can really be anything, eg, a single time point from a normal resolution fMRI, but it could also be an anatomical if you wanted to collect that. doug On 02/25/2013 02:39 PM, SHAHIN NASR wrote: Hi, We are planning to collect high resolution _functional_ MRI for a group of subjects with voxel size smaller than 1 mm. For these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size. The question is, do we need to re-collect _anatomical_ scans for these subjects with smaller voxel size (e.g. 0.5 x 0.5 x 0.5) or we can still use the old anatomical data for co-registration with freesurfer. P.S.: We usually analyze our subjects in native space but technically we can do this in fsaverage space. So, we only need this co-registration for pre-processing and mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] FreeSurfer recon-all two sets of error
try looking at the lh.inflated.nofix or lh.orig.nofix (or rh, whichever one is running) and see if something is dramatically wrong (like skull attached to brain, or hemis connected, etc) On Mon, 25 Feb 2013, Blessy M wrote: Recon is still running. I started the process on 2/21/2013. Its been 4 days. I ran this command, and viewed the aseg file, and that looks reasonable tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg Currently it is at this stage: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 124766 ambiguous faces found in tessellation segmenting defects... .. 61 defects to be corrected 0 vertices coincident .. .. CORRECTING DEFECT 31 (vertices=244, convex hull=142) After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory (-27) = -21 CORRECTING DEFECT 32 (vertices=44865, convex hull=8969) On Fri, Feb 22, 2013 at 5:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I don't think either one of these are errors, just warnings that occur pretty frequently and I don't think should impact the results. Does the recon finish? Do the results look ok? On Fri, 22 Feb 2013, Blessy M wrote: I am getting the bottom two sets of errors while doing a simple recon-all. More specifically while running this command: recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 -autorecon3 Has someone encountered this kind of errors? Is there a fix? 1) Computing MAP estimate using 2772 samples... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 7296.5 tol 0.10 ... ... 2) unfolding failed - restoring original position 0146: dt=13.779160, rms=0.814 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.814, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101542.133 ms iter 0, gcam-neg = 801 .. unfolding failed - restoring original position 0158: dt=13.828393, rms=0.814 (-0.069%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... : dt=0.000, rms=0.814, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100610.148 ms 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Remove medial wall label from surface?
Hi Andries you could use the cutting tools in tksurfer, although it sounds like this is something that we might want to make easier to do automatically. cheers Bruce On Mon, 25 Feb 2013, Andries R. Van Der Leij wrote: Dear all, I am trying to prepare freesurfer surfaces for probtrackx fibertracking. I use the pial surfaces to stop fibers from going back into the white matter. In order to be able to track between hemispheres, the medial_wall labels have to be removed from these pial surfaces. I have difficulties finding out how to accomplish this. Is it possible to 'mask out' the medial wall label from the *h.pial surface, removing all the vertices and thus creating 'holes' in the surfaces? Thank you very much, Andries van der Leij ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] TRACULA trac-all -path giving 'Segmentation error (core dumped) error'
Hi FreeSurfer Community, I am trying to run TRACULA's last step, 'trac-all -path -c path-to-dmrirc-config-script', and am receiving the error: Segmentation fault(core dumped) Moreover, when I look to standard output (terminal), I noticed that the initial 'dmri_paths' command is incomplete. The terminal shows that the command includes the '--init' switch and several arguments (e.g. 'subject ID/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'), the last of which is terminated mid-pathname. Can anyone suggest a reason why this would be the case? Thank you, Susie Kuo ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] TRACULA trac-all -path giving 'Segmentation error (core dumped) error'
Hi Susan - Can you please send your entire trac-all.log? I'll need to see what else was going on before the error message occurred. Thanks, a.y On Mon, 25 Feb 2013, Susan Kuo wrote: Hi FreeSurfer Community, I am trying to run TRACULA's last step, 'trac-all -path -c path-to-dmrirc-config-script', and am receiving the error: Segmentation fault(core dumped) Moreover, when I look to standard output (terminal), I noticed that the initial 'dmri_paths' command is incomplete. The terminal shows that the command includes the '--init' switch and several arguments (e.g. 'subject ID/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'), the last of which is terminated mid-pathname. Can anyone suggest a reason why this would be the case? Thank you, Susie Kuo ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] TRACULA trac-all -path giving 'Segmentation error (core dumped) error'
It looks to me like there was an error at an earlier stage, in the -prior step, so some of the files that the -path step is looking for are not correct. Look for img2imgcoord: Command not found. That's a command from FSL that it can't find. (The 5.2 version of trac-all will not use this any more, BTW.) On Mon, 25 Feb 2013, Susan Kuo wrote: Yes - I'm attaching the trac-all.log. The failure occurred right above this line: 'trac-paths finished without error at Mon Feb 25 14:08:44 EST 2013' if you want to search through the text. The terminal actually showed 2 errors (only the second is recorded in trac-all.log: 1 - 'Segmentation fault (core dumped)' ---mentioned previously and 2 - 'ERROR: must specify input volume(s)' -- which I receive after the program tries to run the below command, *** /usr/local/freesurfer/bin/dmri_mergepaths --indir/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa th --in --out/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa th/merged_avg33_mni_flt.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s) *** I'm currently re-running priors and using 32 training subjects plus the subject's data. Any insight you can offer would be appreciated. Thank you for your help! Susie On Mon, Feb 25, 2013 at 3:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Can you please send your entire trac-all.log? I'll need to see what else was going on before the error message occurred. Thanks, a.y On Mon, 25 Feb 2013, Susan Kuo wrote: Hi FreeSurfer Community, I am trying to run TRACULA's last step, 'trac-all -path -c path-to-dmrirc-config-script', and am receiving the error: Segmentation fault(core dumped) Moreover, when I look to standard output (terminal), I noticed that the initial 'dmri_paths' command is incomplete. The terminal shows that the command includes the '--init' switch and several arguments (e.g. 'subject ID/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'), the last of which is terminated mid-pathname. Can anyone suggest a reason why this would be the case? Thank you, Susie Kuo 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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..
Hi! It turns out the 3T scans have a lot of susceptibility artifact so it might not be the registration failing but more of the signal :( Unfortunately I will just leave out those ROIs for my analysis.. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 3:28 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. It may be that there is a lot of T2* decay around the edge of the brain. See slide 13 from this presentation: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fs.multimodal-integration.ppt To check your data, turn off the intensity normalization by clicking in the image window and hitting 'i'. In the control window, increase the value of fmov to brighten the image. It may be that there is actually tissue outside of those areas but they are very dark. Adjusting the fmov will also allow you to get better contrast which may help to evaluate whether the surfaces inside the brain are correct. doug ps. what was your TE and echo spacing? Is this at 3T? On 02/25/2013 02:52 PM, Sudhin A. Shah wrote: w/attachment From: Sudhin A. Shah Sent: Monday, February 25, 2013 2:52 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Here is the last subject - coronal view.. This is where I started scaling/stretching :( From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah [sut2...@med.cornell.edu] Sent: Monday, February 25, 2013 1:29 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Here is another example registration (different subject). Here I cannot extract values for label 1006 and 2006.. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah [sut2...@med.cornell.edu] Sent: Monday, February 25, 2013 12:49 PM To: Douglas N Greve Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. Sorry - this doesn't look bad. Still I cannot extract values for the ROI label 2013.. On Feb 25, 2013, at 12:43 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It does not look bad to me. Why do you think it looks wrong? On 02/25/2013 12:29 PM, Sudhin A. Shah wrote: Hi Doug, Here's an example view... It looks fine to me. See attached.. From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 12:12 PM To: Sudhin A. Shah Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. The cost (from .mincost) looks fine. Can you send a pic of the registration inaccuracy? doug On 02/25/2013 11:53 AM, Sudhin A. Shah wrote: Hi Doug, Is the BBR cost function in anat2exf.register.dat.bbr.init? mwtp5 3.75 4.00 0.15 9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00 2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01 2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01 0 0 0 1 round Or in anat2exf.register.dat.mincost 0.545185 785.020257 804.709380 1.199352 This looks ok under manual inspection - although the head was not in an ideal position (patient data). However, I cannot extract data from ROI label 2013. Thanks, From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, February 25, 2013 11:39 AM To: Sudhin A. Shah; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix.. First check the value of the BBR cost function. If it is over .8, then something is wrong. To check whether it is an LR flip, you can flip the volume LR and re-run the registration to see if it gets better. doug On 02/25/2013 11:19 AM, Sudhin A. Shah wrote: Hi Doug, When I initially pulled out the correlation values (using the matlab code below) after the automated registration process: regfeat2anat aseg2feat, some ROIS reported NaNs. When I manually checked the registration and adjusted it using tkregister2, I found myself stretching/scaling to make it fit. Consequently I do not have NaNs BUT I am now realising that I should'nt have to scale. 1) How can I check if left-right reversals have happened - its not obvious by eye 2) I am going to re-run
Re: [Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open
Hi Zeke, Thank you for the advice. I have Mac OS X Version 10.7.5. I checked to see if XQuartz is installed and it is. I reinstalled it to be sure but I'm still running into the same problems. Do you (or does anyone else) have other ideas about what could be causing this issue? Thanks, Daniel On Thu, Feb 21, 2013 at 5:22 PM, zkauf...@nmr.mgh.harvard.edu wrote: Daniel, What operating system are you on? If your using MacOS, you must have XQuartz installed in order to use the the Tkregister2/Tksurfer/Tkmedit tools. Check the Application-Utilities folder to see if its already installed. If not, you can download it from here: http://xquartz.macosforge.org/landing/ If your are on Linux than I am sorry but someone else will have to chime in with a potential solution. -Zeke Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f or tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS the command gets stuck on Opening window SUBJECT01. I've also tried just opening tksurfer and tkmedit but the terminal produces no output/windows opening and simply freezes. Any ideas to why this could be occurring? I've let it sit at this stage for multiple hours without anything popping up and without any errors. Thanks! Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ Freesurfer mailing list Freesurfer@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. -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open
have you rebooted since installing XQuartz? i've found a reboot is necessary to get Terminal to open up again. N. On Mon, 2013-02-25 at 17:07 -0500, Daniel Cole wrote: Hi Zeke, Thank you for the advice. I have Mac OS X Version 10.7.5. I checked to see if XQuartz is installed and it is. I reinstalled it to be sure but I'm still running into the same problems. Do you (or does anyone else) have other ideas about what could be causing this issue? Thanks, Daniel On Thu, Feb 21, 2013 at 5:22 PM, zkauf...@nmr.mgh.harvard.edu wrote: Daniel, What operating system are you on? If your using MacOS, you must have XQuartz installed in order to use the the Tkregister2/Tksurfer/Tkmedit tools. Check the Application-Utilities folder to see if its already installed. If not, you can download it from here: http://xquartz.macosforge.org/landing/ If your are on Linux than I am sorry but someone else will have to chime in with a potential solution. -Zeke Hello freesurfers, I just ran registration of my functional images and am trying to visualize the registration for assessment. However, when I use the commands tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f or tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov $FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS the command gets stuck on Opening window SUBJECT01. I've also tried just opening tksurfer and tkmedit but the terminal produces no output/windows opening and simply freezes. Any ideas to why this could be occurring? I've let it sit at this stage for multiple hours without anything popping up and without any errors. Thanks! Daniel -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ Freesurfer mailing list Freesurfer@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. -- Daniel Cole University of Rochester Brain and Cognitive Sciences dcol...@u.rochester.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] blend own template into FS pipeline
Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] blend own template into FS pipeline
Hi Kev for what purpose? If it's just for talairaching, Avi (ccd) is the person to ask cheers Bruce On Mon, 25 Feb 2013, Schumman Resonance wrote: Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Freesurfer problem on Amazon EC2
Dear Freesurfers, I tried to install freesurfer on amazon EC2 as instructed on the wiki page. Everything went well except that mri_* tools like mri_convert doesn't work. When calling it, it returns nothing.\ I also tried to make another Centos instance and install freesurfer manuall, but the same problem existed. I am trying to use it via ssh (ssh to the server and then enter the freesurfer commands). Any suggestions? And is it fast enough to use FS on Amazon micro instance? On my PC freesurfer takes around 35-40 hours for the whole process. Grazie, Tawfik -- Sent with Sparrow (http://www.sparrowmailapp.com/?sig) ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] blend own template into FS pipeline
I would like to play with both normalization and registration steps, and contrast results. Thanks, Kev On Mon, Feb 25, 2013 at 6:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Kev for what purpose? If it's just for talairaching, Avi (ccd) is the person to ask cheers Bruce On Mon, 25 Feb 2013, Schumman Resonance wrote: Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev 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/**compliancelinehttp://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. ___ Freesurfer mailing list Freesurfer@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.
