Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Problem with visualising hippocampal subfield segmentation
by Ed Gronenschild 05 Apr '12

05 Apr '12

Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed

2 8

Custom Fill does not fill
by Kiley Seymour 02 Apr '12

02 Apr '12

Dear experts I have just completed all of the steps leading up to overlaying retinotopy activation on an inflated brain. I have been able to Make a Closed Path, but unfortunately when I press the Custom Fill nothing happens. Any ideas why this is the case. I have been using tksurfer-sess -c polar -a rtopy.self.lh -s Subject1 Thanks. Kiley

3 4

Tracula Siemens DTI
by Gabor Perlaki 02 Apr '12

02 Apr '12

Dear Freesurfers, I have DTI images acquired on a Siemens 3T TIM Trio (software version VB17A). 1, Is TRACULA able to extract the correct b-values and b-vectors from the DICOM headers of Siemens IMA files or do I need to specify them? 2, I'm not sure whether the gradient directions are stored in the image- or in the scanner coordinate system in the headers of Siemens IMA files. Does anybody have any experience with this version of Syngo software (VB17A)? Does TRACULA need the b-vecs in the image or in the scanner coordinate system? Is it able to reorient the bvecs if they are stored in the wrong coordinate system in the header? 3, My DTI protocol (30 diffusion weighted directions and 1 b0) was repeated twice (in separate series, the second right after the first one, same orientation). Because I'd like to correct for eddy current and movement I don't want to average them on the scanner. Is it possible to put the 62 volume (30+30 diffusion weighted directions and 2 b0) into the same TRACULA evaluation in dicom format or do I need to convert them into a single niftii file? Thanks a lot, Gabor

2 1

white-gray contrast algorithm
by John Fredy 01 Apr '12

01 Apr '12

Hello all, I am looking for a white-gray matter contrast algorithm I see the publication: Individual Differences in Verbal Abilities Associated with Regional Blurring of the Left Gray and White Matter Boundary http://www.ncbi.nlm.nih.gov/pubmed/22031871 But,how I can obtain the coordinates of the interface between gray and white matter? Thanks in advance

3 3

masks from fsaverage label into Group FSL Feat
by Michelle Umali 31 Mar '12

31 Mar '12

Hi Freesurfers, I've done a group feat analysis in FSL and I'd like to do an ROI analysis of V1/V2. I've also done recon-all on all my subjects. How would one generate the V1 and V2 binary masks from the fsaverage brain and then register it to the common MNI-152 brain used for the group feat analysis? Could I then multiply the registered binary masks and the zstat.nii.gz from the feat results to get the mean Z-score for that ROI using fslstats? Thanks. Michelle

1 0

How do I use "Subject Exclusions" in qdec
by Brain Apprentice 31 Mar '12

31 Mar '12

Hello Surfers, I am trying to do a qdec analysis and I am working with several hundred subjects. I have my data divided up into different time points and a discrete factor called time. I would like to look at just time 1, then time 2, then time 3. I know how to exclude individual scans by right clicking on a scan and selecting "Exclude" in the qdec pop-up window. What I was wondering is if I could select for exclusion all subjects at once, using the Subject Exclusions windows, that are not time 1. Thanks, Tracy

2 1

qdec...again
by Ahmed, F, Me <fahmed＠sun.ac.za> 31 Mar '12

31 Mar '12

Hello, I got this error while trying to generate the stats table on qdec on my own data: What I don't understand is for the 1st error, where it says it can't locate aseg.stats for 240, the aseg.stats file is in subject 240's file. But what is the reason for the 2nd error? asegstats2table --meas volume --tablefile /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/PTSD_Qdec_Analysis/qdec/stats_tables/aseg.volume.stats.dat --subjects 240 239 165 178 168 169 176 170 177 180 181 187 199 203 206 151 210 208 209 211 212 242 215 219 220 226 229 244 243 249 254 248 255 250 252 246 261 262 265 268 273 279 280 282 283 291 292 294 297 298 299 300 289 Building the table.. SUBJECTS_DIR : /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/PTSD_Qdec_Analysis ERROR: cannot find /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/PTSD_Qdec_Analysis/240/stats/aseg.stats Use --skip flag if you want to continue in such cases ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0xbc320e8): Script: vtkTemp3 GenerateStatsDataTables Returned Error on line 1: Any help would be greatly appreciated. Thanks, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

2 1

Cortical GM in aseg.stats vs. aparc.stats
by Dhinakaran Chinappen 30 Mar '12

30 Mar '12

Dear all, If I sum up the Gray Matter Volume (GrayVol) in aparc.stats for left (or right) hemisphere for all the regions, am I expecting that number to be different from the volume of the Left-Cerebral-Cortex (or Right-Cerebral-Cortex)? Am I correct in assuming that Left-Cerebral-Cortex is the same of lhCortex (lhCortexVol)? Are they anatomically equivalent? I have tried to sum up the GrayVol in aparc.stats for a few cases and obtained a number smaller than the volume of the Cerebral Cortex. Is that expected? Thank you in advance for your clarification, Dhinakaran.

1 0

roi-to-roi functional connectivity analysis
by Lingqiang Kong 30 Mar '12

30 Mar '12

Hi Surfers, Has anyone done ROI-to-ROI functional connectivity analysis using Freesurfer? Current FC pipeline computes the seed-to-voxel correlation for each voxel and thus generates a whole brain correlation map. Is there an easy way to compute the 0-lag correlation between the average time course of two ROIs? One way I presume can work is to take the average time courses generated from the fcseed-sess and do it by hand. For example, just compute the correlation coefficient between "lh.hippo.dat" and "rh.hippo.dat". But does that regress out the white matter and ventricles? Is there a way to do this properly? What should go to the mkanalysis-sess in this case? Thank you for your help. Lingqiang -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/

2 1

annotation file to MNI space
by Yolanda Vives 30 Mar '12

30 Mar '12

Dear Freesurfer experts, I would like to transform the aparc.annot file into MNI space in order to map the parcels from this file to the MNI152_T1_1mm atlas. I have tried the following unsuccessfully: ./mri_label2vol --annot lh.aparc.annot --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_annotation.nii.gz --identity --hemi lh ./mri_vol2vol --targ lh_annotation.nii.gz --mov MNI152_T1_1mm.brain.nii.gz --o lh_annot_MNI.nii --reg $FREESURFER_HOME/average/mni152.register.dat --inv Could you please help me? Thank you in advance, yolanda

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Freesurfer March 2012