Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

testing FS installation - apparent cursor RAS coordinate mismatch?
by Antonio Algaze Beato 09 Jun '17

09 Jun '17

Hello, I just installed FS 6 (mac OS) and followed Examples 1, 2, 3 and 4 under the "Test your FreeSurfer Installation" section here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I am getting a very different view of bert's brain when the cursor RAS coordinates are made to coincide with those on the figure shown in the tutorial. Is this a sign of a failed installation test? Thanks a lot for your help! Antonio

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Re: [Freesurfer] FW: F and p- values for non sig findings {Disarmed}
by Douglas Greve 09 Jun '17

09 Jun '17

Those will have the vertex-wise p-values. You can read them in to matlab with the MRIread() command. On 6/7/17 8:18 AM, Lim, Lena wrote: > > Dear Doug, > > Thanks very much for your reply. > > Sorry, I couldn’t read the files—would they show the non-significant F > and p values as I would find in the summary output if the results were > significant? Please could you kindly help? > > Many thanks again, > > Lena > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* 08 May 2017 16:03 > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] F and p- values for non sig findings > > If you look in the output folder, there will be a subfolder for each > contrast. In there there will be sig.mgh and F.mgh files > > On 5/8/17 9:06 AM, Lim, Lena wrote: > > Dear Freesurfer experts, > > I tried to do a group x gender interaction in QDEC and there is no > sig interaction, but how do I get the F or T and P values please > as requested by the reviewers? > > Many thanks, > > Lena > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > *MailScanner has detected a possible fraud attempt from > "emea01.safelinks.protection.outlook.com" claiming to be* > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr…> >

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How to process ANCOVA with age as covariate
by Gwang-Won Kim 09 Jun '17

09 Jun '17

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How to do a regular GLM in 2 groups with 2 times
by llkxbb＠sina.com 09 Jun '17

09 Jun '17

Dear FS Experts,I want to measure the thickness difference between two groups, control and experimental group. And every subject scaned twice.I look at the page: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessingand some reply in Mail-list.I looked one method: Subtract time2 to time1 manually and do a regular GLM.How to substract times? Maybe the results after the cmd are? "recon-all -base con* -tp con*_MR1 -tp con*_MR2 -all recon-all -base sub* -tp sub*_MR1 -tp sub*_MR2 -all" Can I do GLM between con* and sub* directly?Could you please tell me how to do? Many thanks!Best regards,Melody

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Outputs from 5.3 to 6.0
by Manuel Delgado 09 Jun '17

09 Jun '17

Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

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HIPS unsupported
by Jens Offenbach 09 Jun '17

09 Jun '17

Hallo, I have finished my test runs and have observed that using export DIAG=0xFFFFFFFF and export DIAG_VERBOSE=1 cause all recon-all runs to fail with the following error: HIPS unsupported No such file or directory I have tested different computing environments (container, hardware, VMs) using my shrinked freesurfer archive and the release archive of FreeSurfer 6.0.0 on Ubuntu 16.04.2 LTS... The issue occurrs with both archives and seems to be reproducible. Another problem is, that the analysis runs take much longer when the diagnosis level has been set. A (very big) archive of a broken run has been uploaded. I had some trouble during upload. The file is named "OAS1_001_MR1.tar.gz" and can be found in "transfer/incoming" of your FTP-server. May someone please have a look? Thank you very much! Regards, Jens

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-openmp flag in mri_em_register
by Lisa Kramarenko 08 Jun '17

08 Jun '17

Hello, I am using HCP pipelines and I would like mri_em_register which is being called from a pipeline script to run on 2 cores instead on all available ones. I tried to just add an -openmp flag to the command as suggested here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.html my command looks like this: mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz "$SubjectDIR"/"$SubjectID"/mri/nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca "$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta -openmp 2 yet I get an error: mri_em_register: could not open GCA -openmp Do you have an idea of how to fix it? Thanks! Lisa

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[TRACULA] Issue with registration to diffusion space
by Ostrowski, Lauren 08 Jun '17

08 Jun '17

Hello experts, I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it? Thanks, Lauren Ostrowski

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Re: [Freesurfer] FW: Freeview Application
by zkaufman＠nmr.mgh.harvard.edu 08 Jun '17

08 Jun '17

Recently Microsoft announced bash on Windows and initial tests within our group have shown that freesurfer and freeview work in this environment: https://msdn.microsoft.com/en-us/commandline/wsl/about However, currently freeview is not shipped as a separate stand-alone package from freesurfer. However, this could probably be done with a small amount of effort. If this is something of general interest perhaps I can add this stand-alone package to the Download page. -Zeke > Just wanted to re-circulate this. > Thanks in advance! > > Panos > > Panagiotis Fotiadis > Research Technologist II > J. P. Kistler Stroke Research Center > Massachusetts General Hospital > 175 Cambridge Street, Suite 300 > Boston, MA, 02114 > T: (617) 643-3869 > ________________________________ > From: Fotiadis, Panagiotis > Sent: Monday, June 05, 2017 1:14 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Freeview Application > > Hello FS team, > > Is there any way to download FreeView as a standalone application on a > Windows computer, or would I need to download freesurfer as a whole and > then VPN? > > Thanks in advance! > Panos > > Panagiotis Fotiadis > Research Technologist II > J. P. Kistler Stroke Research Center > Massachusetts General Hospital > 175 Cambridge Street, Suite 300 > Boston, MA, 02114 > T: (617) 643-3869 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview Application
by Fotiadis, Panagiotis 08 Jun '17

08 Jun '17

Hello FS team, Is there any way to download FreeView as a standalone application on a Windows computer, or would I need to download freesurfer as a whole and then VPN? Thanks in advance! Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA, 02114 T: (617) 643-3869

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Freesurfer June 2017