Freesurfer

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30088 discussions

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

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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.

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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.

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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/

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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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problem in building cortex mask
by lorenzo pasquini 30 Mar '12

30 Mar '12

Dear freesurfers, I have a problem in creating masks of the left and right cerebral cortexes. The message "found 0 values in range" is displayed and an empty mask is created. This is surprising as I am able to build masks of the right and left hippocampi and entorhinal cortexes using the same command without any problems. Further the satistic file aseg.stats indicates me a huge amount of voxels in the cerebral cortexes. I am using the segmentation ID 3 for the left cerebral corex and 42 or 53 for the right cerebral cortex. I am surprised as well to find two different IDs for the same region, 42 comes from the aseg.stats file, 53 comes from the FreesurferColorLUT table. Wich ID is the right one to use?Why can I build masks of hippocampal regions but not of the cerebral cortexes? Thank you very much and kind regards, Lorenzo Pasquini

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Now Hiring: Postdoc
by Juranek, Jenifer 30 Mar '12

30 Mar '12

We have a current opening for a post-doctoral associate in the areas of *image analysis* (structural and functional) and *developmental neuroscience*. Available resources include a research-dedicated 3.0T MRI scanner and analysis platforms based in MATLAB/UNIX. The successful candidate will be expected to work independently (with some supervision) to analyze multimodal neuroimaging data (volumetrics, cortical thickness, DTI, resting state connectivity with fMRI and MEG/EEG, lesion identification and analysis) obtained from typically-developing and atypically developing pediatric study participants. The successful candidate should have a strong publication record and a continued interest preparing manuscripts for publication in the field of pediatric neuroimaging using multimodal imaging data. The successful candidate should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of multimodal neuroimaging data. Experience with Freesurfer, FSL UNIX/LINUX/ and/or programming skills (MATLAB; Perl; bash) are highly desirable. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Dr. Juranek at Jenifer.Juranek(a)uth.tmc.edu<mailto:Jenifer.Juranek@uth.tmc.edu>. This position is currently available; the search for a successful applicant will continue until the position is filled. ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD Assistant Professor UT Houston Developmental Pediatrics Children's Learning Institute Voice: 713.500.3813 Fax: 713.500.3878

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base.mgh file
by Tina Jeon 30 Mar '12

30 Mar '12

Freesurfer universe, I noticed that the newer version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon Biomedical Engineering Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center P: (214) 645-2892 F: (214) 645-2885 ________________________________ UT Southwestern Medical Center The future of medicine, today.

1 0

ICV estimation
by HOSSU Gabriela 30 Mar '12

30 Mar '12

Dear all, I am working with FreeSurfer version 5.10 from 2 months. I am interested in hippocampus volume measurements and I want to normalize them with the intracranial volume. We have scanned about 4 times the same 2 healthy subjects (3T GE HDxt, 8 channel coil). 3D acquisitions were made with the BRAVO GE sequence in coronal and sagittal planes (roughly with the same parameters) . On the hippocampus we obtained about 5% intra subject variation but for the ICV intra subject variation is around 15%. With the supra tentorial volume estimations, the variation is around 2%. Any idea to explain this so important difference for the ICV estimation? Can we use the supra tentorial volume in order to normalize our hippocampus estimations? Thanks, Gabriela HOSSU, Ph.D. Chef de projet CIC-IT Nancy (Inserm CIT801) CHU de Nancy Brabois 4ème étage Tour Drouet Rue du Morvan 54511 VANDOEUVRE-LES-NANCY FRANCE

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selxavg3-sess error
by Oya, Hiroyuki (UI Health Care) 30 Mar '12

30 Mar '12

Hi I got an error while running selxavg3-sess, "cannot find AFNI command 3dvolreg".(In ubuntu v11.). Any help would be appreciated. Hiroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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