Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

FreeSurferColorLUT labels
by Susan Alice McLaughlin 26 Feb '13

26 Feb '13

Hi, In FreeSurferColorLUT.txt (Freesurfer 5.1), there is a label for the inferior colliculus (7100), but this structure seems only to be labeled collectively with other brainstem structures (16) in aparc.a2009s+aseg. It appears from posts in the mail list that only a subset of the labels in FreeSurferColorLUT.txt make it into the automatic segmentation done by recon-all. Any suggestions of how I could access lh and rh inferior colliculus labels for fsaverage, and then morph them to each subject's norm.mgz? Thanks, Susan McLaughlin SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Mean intensity values
by Hunt, Sarah C 26 Feb '13

26 Feb '13

Hello, I recently ran freesurfer on a group of patients and controls, and have found a statistically significant difference between groups in the mean intensities of certain grey-matter regions (the grey matter volumes of these regions are not statistically different.) Mean intensity values were extracted using the command: asegstats2table \ --subjects ... \ --meas mean \ --tablefile aseg.mean-intensity.table What do the mean intensity values of the grey matter represent? Are they representative of a neuroanatomical property of the grey matter? Thanks, Sarah

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Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned
by Ed Gronenschild 26 Feb '13

26 Feb '13

Hi Doug, The condition numbers were: - 1e+08 for problematic fsgd file - 371.233 for previous fsgd file I tried also v5.1, however with no succes. The matirx was still ill-conditioned with condition number 2.80809e+07. Cheers, Ed On 1 Feb 2013, at 9:53, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 12 > Date: Thu, 31 Jan 2013 14:08:11 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Problem with glmfit: matrix is > ill-conditioned > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <510AC11B.4090902(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Ed, that sounds strange. What were the condition numbers for the > two > analyses? This should be printed out into the terminal. It is also > possible that it is a scaling issue. This should not be an issue in > 5.1, > but it is possible that it could have an effect if two columns are > very > similar. > doug > > > On 01/30/2013 05:10 AM, Ed Gronenschild wrote: >> >> Hi Doug, >> >> It is indeed correct that columns 1 and 17 are highly correlated. >> However, >> for another version of the fsgd file, where the corresponding >> class and >> covariate values where identical but with other covariates (so >> leading to >> the same columns 1 and 17, other columns are different), all went >> well. >> So probably some other columns are highly correlated as well. >> Anyway, what can we do about it? Just leave the offending covariate >> (s) >> out? >> >> Cheers, >> Ed >> >> >> >>> Message: 1 >>> Date: Thu, 24 Jan 2013 12:51:23 -0500 >>> From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu >>> <mailto:greve@nmr.mgh.harvard.edu>> >>> Subject: Re: [Freesurfer] Problem with glmfit: matrix is >>> ill-conditioned >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <5101749B.4060305(a)nmr.mgh.harvard.edu >>> <mailto:5101749B.4060305@nmr.mgh.harvard.edu>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> Hi Ed, the problem is that your covariates are highly correlated. >>> Eg, >>> column 1 is nearly identical to column 17. >>> doug >>> >>> >>> On 01/24/2013 06:36 AM, Ed Gronenschild wrote: >>>> Hi, >>>> >>>> Running mri_glmfit ( v5.0.0, Mac OSX10.6) I got he following >>>> error message: >>>> >>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>> Possible problem with experimental design: >>>> Check for duplicate entries and/or lack of range of >>>> continuous variables within a class. >>>> If you seek help with this problem, make sure to send: >>>> 1. Your command line: >>>> mri_glmfit --y lh.sib_con_cann_aangepast3.thickness.sm0.mgh >>>> --fsgd >>>> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ >>>> fsgd_sib_con_cann_aangepast3.fsgd >>>> dods --glmdir lh.sib_con_cann_aangepast3.dods.sm0.glmdir --surf >>>> fsaverage lh --C >>>> ../../STATS/FSGD/age_gender_scan_educ_hand_cannabis/ >>>> group_thickness_gender_scan_age_educ_hand_cann.mtx >>>> >>>> 2. The FSGD file (if using one) >>>> 3. And the design matrix above >>>> >>>> Please find attached the requested files. >>>> >>>> I noticed that rows 68 and 147 of the matrix Xg.dat are identical, >>>> and most probably caused the error. >>>> In the fsgd file I see that the correspondig cases indeed have >>>> identical values, although they are referring to different data. >>>> How to proceed? >>>> >>>> Cheers, >>>> Ed >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ > greve/

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Re: [Freesurfer] extracting hand drawn ROIs to Afni space
by Douglas N Greve 26 Feb '13

26 Feb '13

Hi Paul, I'm not sure I understand. What does 3dcalc have to do with the LUT? doug On 02/25/2013 05:13 PM, Paul Beach wrote: > Hi Doug. Thank you for the e-mail. > > I do, actually, have a 'next step' problem. > > I've been able to get ROIs drawn in tksurfer into an augmented > aparc+aseg file of an averaged subject. Now 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 that utilizes their place in > the LUT. However, I have the problem of needing to export the 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 > > > > On Mon, Feb 25, 2013 at 11:28 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > 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 > > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@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 Q&A 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(a)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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Pipeline Question(s) for mri_ca_train
by Douglas N Greve 26 Feb '13

26 Feb '13

Hi Daniel, I'm reposting this to the FS list because I don't really use mri_ca_train. doug On 02/26/2013 02:45 PM, Barron, Daniel S wrote: > Hello Dr. Greve, > > I am trying to create a .gca for thalamic nuclei. Based on the Morel > 2007 atlas, I have created 6 nuclear grouping masks per hemisphere. I > created these masks in MNI space with fslmaths. Each mask is a > separate, binary .nii.gz. > > In preparation for mri_ca_train, I have converted the .nii.gz files to > .label files with mri_cor2label. However, I am unable to assign > vertex numbers for each voxel (because the thalamic volumes do not > correspond to a surface?). When I transform the binary > .nii.gz-->label files, in each .label the entire vertex number column > reads "-1". I have attached one such label as .label.txt. This > carries over even after I register each to FreeSurfer space > (mri_label2label). The problem is when I go to create an annotation > file, I get an error saying the vertex number is -1. Can you > recommend a way for me to navigate this error? > > Once I have created the annotation file, can I use mri_aparc2aseg to > create the segmentation files for mri_ca_train? mri_aparc2aseg --help > says this is intended for surface annotations; I want to use it for > volumetric annotation. > > Thank you very much for your help~ > > Cheers, > Daniel > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mgh conversion
by Douglas N Greve 26 Feb '13

26 Feb '13

I think you can analyze the data in SPM as long as you don't do anything that makes assumptions about the spatial organization of the data (eg, spatial smoothing or clustering). doug On 02/26/2013 11:18 AM, Glen Lee wrote: > Hi Doug > Many thanks for clarification. > Yes, I was hoping to run GLM on the 2D surface data in the pipeline of > SPM suite. > Here is my question: > -the 2D surface EPIs were converted from 3D volumes. > - if the 2D data are converted back to the 3D volume > using mri_surf2vol, then it'd be circular right? > > I'm hoping to find out a way of faking SPM so that it thinks it's > analyzing the 3D, but indeed the data are 2D. > Then, I can take advantage of SPM to get SPM.mat file and mask image > that would be necessary for other analyses. > > I'd be grateful if you answer my questions once again. > Glen > > > > On Mon, Feb 25, 2013 at 11:01 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > 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 > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] problem with trac-all -prep proc stage
by Anastasia Yendiki 26 Feb '13

26 Feb '13

Make sure doregcvs is not set to 1 in your config file. This option is not meant to be used in 5.1 but will be in 5.2. On Tue, 26 Feb 2013, Jon Wieser wrote: > hi anastasia, > i don't know what "CVS for inter-subject registration " is. > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, February 26, 2013 1:32:34 PM > Subject: Re: [Freesurfer] problem with trac-all -prep proc stage > > > Hi Jon - Are you trying to use CVS for inter-subject registration? > > a.y > > On Tue, 26 Feb 2013, Jon Wieser wrote: > >> hello >> >> i ran a trac-all -prep -c ./dmrirc_single_subject and got the following error: >> >> >> flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.flt.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.bbr.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2anat.mat >> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat >> ln -sfn /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/cvs/cvs_avg35 /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs >> mri_cvs_register --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs >> >> Log file is freesurfer_to_cvs_avg35.mri_cvs_register.1302261152.log >> >> Tue Feb 26 11:52:22 CST 2013 >> --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs >> $Id: mri_cvs_register,v 1.4.2.2 2010/08/11 17:52:00 nicks Exp $ >> cerebrum.uits.uwm.edu >> Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >> The outdir: >> /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs >> mris_resample --atlas_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/cvs_avg35/surf/lh.sphere --annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/label/lh.aparc.annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.aparc.annot --subject_surf /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.white --subject_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.cvs.tocvs_avg35.sphere.reg --out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.white >> Exception caught while parsing cmd-line >> ambiguous option annot >> Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >> >> trac-preproc exited with ERRORS at Tue Feb 26 11:52:22 CST 2013 >> >> >> >> Jon >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > >

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FreeSurfer recon-all two sets of error
by Blessy M 26 Feb '13

26 Feb '13

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 0.000010 ... ... 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... 0000: 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... 0000: dt=0.000, rms=0.814, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100610.148 ms

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Remove medial wall label from surface?
by Andries R. Van Der Leij 26 Feb '13

26 Feb '13

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

2 3

problem with trac-all -prep proc stage
by Jon Wieser 26 Feb '13

26 Feb '13

hello i ran a trac-all -prep -c ./dmrirc_single_subject and got the following error: flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat ln -sfn /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/cvs/cvs_avg35 /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs mri_cvs_register --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs Log file is freesurfer_to_cvs_avg35.mri_cvs_register.1302261152.log Tue Feb 26 11:52:22 CST 2013 --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs $Id: mri_cvs_register,v 1.4.2.2 2010/08/11 17:52:00 nicks Exp $ cerebrum.uits.uwm.edu Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 The outdir: /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs mris_resample --atlas_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/cvs_avg35/surf/lh.sphere --annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/label/lh.aparc.annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.aparc.annot --subject_surf /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.white --subject_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.cvs.tocvs_avg35.sphere.reg --out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.white Exception caught while parsing cmd-line ambiguous option annot Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Feb 26 11:52:22 CST 2013 Jon

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Freesurfer February 2013