[Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Hi Freesurfer developers, I was looking for the freesurfer command to export hippocampal sufields segmentations but I did not found. What is the command to export this measures and in what folder are exported the file? Thanks a lot. Best, -- *Mi

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Hola Miguel Ángel, What do you mean by exporting? The volumes? There is a command to gather the volumes from all subjects in the subjects directory, which is: quantifyHippocampalSubfields.sh (in FreeSurfer 6.0) quantifyHAsubregions.sh (in dev version)

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Hi Eugenio, I want to export the volumnes of all subjects, I used the quantifyHippocampalSubfields.sh command and apparently it did work but now I can´t find where Freesurfer saved the file. Here is the response of Freesurfer rmnlab1:~ neucoga$ qua

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution The results should be in pruebahipocampo.txt, which will be located in the directory from which you ran the command. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College Lond

[Freesurfer] hippo subfields and amygdala

External Email - Use Caution Hi FS experts, I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the

[Freesurfer] mri_label2label: Empty label file

External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness value of a significant cluster from all the subjects used for a comparison for further statistical analyses. I ran the mri_surfcluster first to create the ROI label with fsaverage and then used mr

Re: [Freesurfer] hippo subfields and amygdala

External Email - Use Caution Hi Erik, The subfield module gives you a segmentation in the same space as brain.mgz and the rest of volumes in the recon-all stream: [lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz You can use mri_extract_label to create binary masks. Cheers, /Eugenio

Re: [Freesurfer] hippo subfields and amygdala

External Email - Use Caution Hi Eugenio, Thanks, I'll give that a try. Just a quick question, the correct ROI id's for each subfield are in the LUT ? Is there a different LUT in the DEV version for the hippo and Amy subdivisions individually and also the anterior /posterior di

Re: [Freesurfer] hippo subfields and amygdala

External Email - Use Caution Yes the LUT evolves but remains backwards compatible. And yes, the command looks OK to me! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http

[Freesurfer] FS-FAST error:

External Email - Use Caution FS-FAST error: analysis language.sm05.lh does not exist, see mkanalysis-sess Hello FreeSurfer Developers, I'm attempting to run FS-FAST on my own data, as described on the FS-FAST tutorial (http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastF

Re: [Freesurfer] hippo subfields and amygdala

External Email - Use Caution Thanks a mill Eugenio, Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 29 May 2018 13:02:07 To: Freesurfer support list Subject: Re: [Freesurfer] hipp

Re: [Freesurfer] mri_label2label: Empty label file

Hi Emmanuel you need to send us the complete command line and screen output of the commands that failed if we are going to help you cheers Bruce On Tue, 29 May 2018, Emmanuel Nwosu wrote: External Email - Use Caution Dear FreeSurfer users, I want to extract the thickness

Re: [Freesurfer] fthresh function in tksurfer

It will be added very soon. I'll let you know when it is ready. Best, Ruopeng On 05/28/2018 05:35 PM, srishti goel wrote: Hi Ruopeng, Thank you so much! That option will be super helpful. Are you planning to add that option to Freeview soon? Best, Srishti Best, Srishti Social/Clinical Res

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Hi Eugenio, I ran the command and fs gave me the following error in all subjects Collecting data for subject: 5250 /Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 94: pruebahipocampo.txt: Permission denied In order to gatherin

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Yes, it looks like that. You can try ~/Desktop/pruebaHipocampo.txt you should be able to write there. -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com h

[Freesurfer] Number of iterations with --cache flag

External Email - Use Caution Dear FreeSurfer Experts, I am wondering how many iterations are run in the precomputed Z Monte Carlo simulation when using the --cache flag with mri_glmfit –sim. Sorry if this has been documented somewhere, I cannot find it – can anyone direct me to

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Thank you Eugenio, it works but now I have a "absurd" question, the volume values that I obtained are mm with six decimals? For example, for the left_Hippocampal_tail I obtained 498.117062 Sorry for this absurd question but I would like be sure about

[Freesurfer] FW: Number of iterations with --cache flag

External Email - Use Caution Sorry, found it! It’s 1 as indicated in the sig.cluster.summary file. Best, Lea Backhausen -- Lea Backhausen Research Assistant Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Ger

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Yes! -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Miguel Ángel Rivas Fernández Reply-To: Freesurfe

Re: [Freesurfer] FW: Number of iterations with --cache flag

Actually, I think 1000 is probably fine. Also, you may wan to use permutation since the monte carlo correciton tends to be too liberal. here are instructions http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 5/29/18 11:37 AM, Backhausen, Lea wrote: Sorry, f

Re: [Freesurfer] mri_label2label: Empty label file

depends on the size of the label and the command you used. A better way to do it is to map all of the individual thickness maps into fsaverage space, and then just use the significant cluster directly. On 5/29/18 6:44 AM, Emmanuel Nwosu wrote: Dear FreeSurfer users, I want to extract the t

Re: [Freesurfer] FS-FAST error:

You called the analysis "my-language..." not "language" . Try using my-language... when running selxavg3-sess On 5/29/18 8:24 AM, 高 寒 wrote: External Email - Use Caution FS-FAST error:analysis language.sm05.lh does not exist, see mkanalysis-sess Hello FreeSurfer Developers, I'm att

Re: [Freesurfer] Contrast interpretation - between-groups mean

On 5/27/18 3:33 PM, Pedro Rosa wrote: Hi, Doug. For this specific 'problematic' cluster, the maximum statistical value from the cluster summary is negative, that indicates a direction of result (considering the contrast matrix I used) opposite to the one I get when I compare means. I inspe

[Freesurfer] QDEC, order of groups for interpretation of results

External Email - Use Caution Hello experts, I am using QDEC to compared LGI values between groups (typically develping and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the following order: Typically developing ASD However, when I upload my qdec.table.dat file o

Re: [Freesurfer] QDEC, order interpretationof Gracias @batmarandua for aqaa

External Email - Use Caution On Tue, May 29, 2018, 20:16 Avi Gharehgazlou wrote: > External Email - Use Caution > > Hello experts, > > I am using QDEC to compared LGI values between groups (typically develping > and ASD). I made a "diagnosis.levels" file, putting my 2 gro

Re: [Freesurfer] fthresh function in tksurfer

External Email - Use Caution Thanks a lot Ruopeng, really appreciate it. Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.go

[Freesurfer] Postdoctoral Scholar positions in neuroimaging

External Email - Use Caution NIDL and brainLENS-east labs (Neurobiology of Individual Differences in Language Lab http://nidl-lab.org, PI: Roeland Hancock PhD; and Laboratory for Learning Engineering and Neural Systems http://brainlens.org, PI: Fumiko Hoeft MD PhD) at University of

[Freesurfer] Installing different versions of FreeSurfer on Same computer (error)

External Email - Use Caution Hello, My Mac has v5.3 installed in the default location ( application). However, whenever I try to install v6.0 in a different location ( desktop) it deletes the existing v5.3 from application. Any solution to this? I’m trying to run the brainstem

Re: [Freesurfer] Installing different versions of FreeSurfer on Same computer (error)

Hello Paul, By default, the mac installer will install freesurfer under /Applications/freesurfer. There is an option to change the install location however, see the screenshots under, https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall It sounds like you ran the 5.3 installer - did not use

[Freesurfer] Subfields Development Version MATLAB:scriptNotAFunction

External Email - Use Caution Hi I’m attempting to run the hippocampal/amygdala subfields segmentation in the most recent daily build of FreeSurfer (Centos7). The T1 only and multispectral variations run fine, but attempting the segmentation without the T1 (USE_T1=0) produces th