Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Can I use specific template for FS computing
by shi yao wang 11 May '17

11 May '17

Dear FS experts: We generated a specific population of brain template. Just wondering if FS can use these templates to measure brain volume. thanks Lawrence Emory

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mean hemispheric value in a .mgh
by Damien MARIE 11 May '17

11 May '17

Hi, I’ve a .mgh that is a volume projected on the surface of the same subject at mid-thickness (output of mri_vol2surf) . I would like to extract the mean hemipheric value in this X.mgh. I guess it is possible with mris_anatomical stats but probably my command line is incorrect (see below). Any advices? Thank you and best, Damien mris_anatomical_stats ct_pp1_N4_bet_MP2RAGEcorr -a ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot lh R1.mgh computing statistics for each annotation in ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot. reading volume /home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/mri/wm.mgz... reading input surface /home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh... ERROR: MRISread: file '/home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!

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Re: [Freesurfer] Freesurfer Digest, Vol 159, Issue 12
by Weisholtz, Daniel S.,M.D. 11 May '17

11 May '17

Dear Bruce, Thank you so much for your suggestions. Unfortunately, I was not able to open lh.defect_labels in freeview. When I try, Freeview crashes. There are no rh surfaces in the surf folder, so I presume this means the problem occurred in the left hemisphere. I was able to view the inflated.nofix and orig.nofix but I’m still not exactly sure what the problem is, and I would be grateful if you could take a look at the subject folder. I will upload it to the ftp site. It is called s117. Thank you! Best, Dan On May 10, 2017, at 10:43 AM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 9 Date: Tue, 9 May 2017 15:54:12 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1705091553090.16219(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-15" Hi Daniel you can load the ?h.defect_labels as an overlay on either the inflated.nofix or orig.nofix surface and use it to find the location of that defect. Usually this means something big is wrong - it should be obvious looking at the inflated.nofix I would think. If you can't find it, upload the subject to our ftp site and I'll take a look Bruce On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote: Hello Freesurfer Developers, I am trying to run recon-all -all and the procedure is freezing while trying to correct what appears to be a large defect (vertices=36706). The source T1 image is not great quality due to rippling artifact, but I have inspected brainmask.mgz, wm.mgz, and aseg.mgz and I cannot identify a large defect. The dura was not completely removed, and I tried improving this by using various watershed thresholds as well as using gcut. I also tried manually removing the remaining dura, but none of this was helpful. ?I also tried using -T2FLAIR, but this did not seem helpful either.? I am attaching the recon-all.log. This does not include the edits I made to brainmask.mgz. That was done on a separate attempt. This does include the -T2FLAIR, as you can see in the recon-all.log file. 1) FreeSurfer version:?freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: OS X Yosemite 10.10.5 3) recon-all.log attached I very much appreciate any assistance you can provide. Happy to send any of the data if it would be helpful. Sincerely, Dan Weisholtz

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Volume comparison between groups and QDEC
by John Anderson 11 May '17

11 May '17

Dear Dr Doug, I have two groups of subjects (80 patients and 40 controls). I analyzed the data using Freesurfer v6.0. I want to study the difference between the groups in "precentral gyrus volume". After "recon-all" I built Qdec table and I used Qdec to compute the comparison by including eTIV a covariate. After correcting the results using Monte Carlo simulation or adjusting for FDR I found no difference between the groups in volume neither in surface area. I adjusted the precentral gyrus volume values for eTIV using the commands: mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017 mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024 I extracted the adjusted volume values to SPSS then I ran box plots comparison between the groups and I found difference at (P<0.0001) Why Qdec doesn't show the difference between the groups although the p value is very small. What I am doing wrong in Qdec? Is it wrong to include eTIV a covariate? Thank you for any advice John

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hippocampal subfields: which are previous step result (files) needed for the process?
by Guido Pascariello 11 May '17

11 May '17

Hi Experts, I am running Freesurfer v6.0 on a Cluster. I've traied this command: *recon-all -i $IMAGEN -s $SUJETO -all -hippocampal-subfields-T1 -brainstem-structures* Although all step in recon-all works fine, hippocampal-subfields process allocate much more RAM than previous step (10 GB of RAM more or less, and take about 30 mins to be completed, according to other post in the forum). I am thinking in run these one after another, in order to not need to reserve a lot of memory for a long period of time (just for optimization) *I want to know which are the files (from recon-all process) that hippocampal-subfields process needs?* Just to be sure that these will be transferred to the node before the process starts. If you please help me Cheers -- *Bioing. Guido Pascariello* Becario Doctoral CIFASIS - CONICET Grupo de Procesamiento de Señales Multimediales http://www.cifasis-conicet.gov.ar/ Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386

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Interpreting PALM-FreeSurfer results
by Sahil Bajaj 10 May '17

10 May '17

Hello FreeSurfer experts, I used PALM toolbox to identify significant clusters after multiple comparison correction using following command: palm -i lh.WASI_LGI.5.mgh -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh -d Xg_WASI_LGI.csv -t Contrast_WASI.csv -m WASI_S5/lh.WASI_LGI.glmdir/mask.mgh -o WASI_S5/ResultsLH_WASI_LGI -C 1.95 -twotail -n 10000 -nouncorrected My output ResultsLH_WASI_LGI_clustere_tstat_fwep.mgz gives me attached screen shot cluster when I open with FreeView. However, I noticed that the colorbar shows values around 0.7 at the red cluster and value 1 elsewhere i.e. values lie between 0 and 1 for the whole brain. (1). From the command and according to previous posts on FreeSurfer forum, I am assuming that significant clusters should be showing value of 1.3 (-logp, where p = 0.05) so I am not sure why the whole brain has value of 1 which is higher than at the red cluster. (2). If significant cluster should show value of 1.3 then isn't it true that the rest of the brain should show values much lower than 1.3 but in actual rest of the brain is showing values higher than 0.7. After displaying partial correlation maps (pcc.mgh), I made sure that the red cluster really has higher correlation than the rest of the brain. I would really appreciate any help if someone could correct me if I am interpreting the results incorrectly? Thanks.

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Obtaining surface normal vector from plial surfaceRAS coordinate
by Jerry Jeyachandra 10 May '17

10 May '17

Hi list, I'd like to extract the surface normal at a location specified in surfaceRAS coordinates after performing segmentation. I know there are methods to extract all vertices and faces then compute face normals from there, but I'm not familiar with methods to relate these to specified coordinates. Thanks Jerry Jeyachandra

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neither NIfTI-1 qform or sform are valid
by shi yao wang 10 May '17

10 May '17

Dear FS experts: There are some error message when I running recon-all as following: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Are there any problem in raw data? I am using MRICRON to convert DICOM to nii thanks Lawrence

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Integrated rectified values
by Yun, Hyuk Jin 10 May '17

10 May '17

Hi Freesurfer team, I wonder how calculate integrated rectified values of a ROI using *mris_anatomical_stats. * After reading lh.*.H.crv, lh.*.K.crv, lh.thickness, and lh.aparc.DKTatlas40.annot files in matlab, I couldn't calculate same output of the results using the command of "mris_anatomical_stats -a ./subj/label/lh.aparc.DKTatlas40.annot -b subj lh" Could you explain how calculate them? A link or paper about this is also helpful. Best, HyukJin

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Re: [Freesurfer] Surface area
by John Anderson 10 May '17

10 May '17

Dear Dr Doug, Thank you very much for the detailed answer! I like very much the idea to adjust surface area by eTIV. Kindly I have the following follow-up questions and I highly appreciate your input: 1. Can this adjustment be done in Qdec by including eTIV a covariate or nauisance factor? 2. The individual ROIs for an external statistical software (e.g. SPSS): Can the adjustment be done by measuring the percent volume or surface relative to eTIV then make the comparison between the groups ( i.e. adjusted ROI volume = ROI volume*100 / eTIV) 3. Which approach is recommended: Adjust volume or surface area by adding eTIV as a confounding factor in surface based analysis (e.g. in Qdec) or by comparing the adjusted volume and surface area for the ROIs in SPSS Regards, John -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, May 8, 2017 5:55 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface area Yes, I would recommend making some kind of adjustment. As with all such adjustments, the adjustment you choose will dictate how you interpret the results (eg, a eTIV adjustment means something different that an adjustment for whole brain volume). For surface area, I usually adjust the eTIV. It might seem strange to adjust surface area by a volume, but for a highly folded surface, the surface area actually goes up linearly with the volume. But adjusting by total surface area is ok too. On 05/08/2017 02:29 PM, John Anderson wrote: > Dear Freesurfer experts, > I know that the grey or white matter volume measures for the ROIs > reported in "wmparc.mgz" can be adjusted for the total intracranial > volume.... Is is correct to do the same for surfaces? I mean can the > surface of an ROI (e.g. precentral) be adjusted to total surface area? > If yes, this must be done for total white right or total left > depending on the ROI if it is left or right, correct? > > Thank you > John > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer May 2017