Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mri_volsynth help
by Mauricio Watanabe Ribeiro 13 Aug '20

13 Aug '20

External Email - Use Caution Hi Freesurfers, I'm trying to create a ROI based on peak significance voxel from a paper. They reported a peak at X=21, Y=-71, Z=22 and area of 4,620 mm², based on MNI305. My idea was creating a sphere ROI around this voxel and check its area in the brain image. To do so I'm using the following command: mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz \ --pdf delta --c_ras 21 -71 22 --res 1 1 1 1 --dim 7 7 7 1 --o ROI.sm00.mgh I also tried with --c_ras 107 106 57, that is the value of this point on brainmask.mgz However, when I visualize the surface created with freeview my ROI is always in the center of the brainmask.mgz. And if I try to smooth this surface using mris_fwhm it exits with error. Can someone help me with this? Thanks, Mauricio

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surf2vol from annotation?
by Ellen Ji 13 Aug '20

13 Aug '20

External Email - Use Caution Dear Freesurfer experts, I have a surface parcellation (annotation) with 318 labels; see attachments for each hemi. I wish to extract volume-based features (FA and MD) corresponding to these 318 labels. I believe I should perform something like surf2vol to extend the labels into FA space. However, my surface parcellation is not a surface overlay (which I need for --so). Any other ways to do this? I wish for the output to be a single volume-based parcellation of 318 labels, corresponding to the two surface parcellation annotation files. I will then use this output to get FA measures for each of the 318 regions. Thank you, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/

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Re-posting about normalization of hippocampal subfields
by Haewon Roh 13 Aug '20

13 Aug '20

External Email - Use Caution Hi. team! Recently, I submitted a paper dealing with volumes of hippocampus and its subfields in epilepsy patients who have significantly reduced hippocampal volume (compared with normal controls) and, in that paper, I used the normalization method using ICV, which was suggested by Jack CR in 1989: normalized volume = volume (observed) – b (ICV – mean ICV), where b is the slope of regression for each ICV. But, one of the reviewers pointed out that I should use the method based on each patient's hippocampus rather than total intracranial volume. Since I've seen that a lot of papers, which dealt about these kinds of issues about hippocampus and subfields, used the same method with me, I am really doubtful that it is more appropriate if I should use the method using individual volume of hippocampus (rather than ICV) in order to normalize its volumes of substructures in the comparison analysis with those of controls. # And, whether this is true or not, could you please recommend to me several literatures that can show which method of normalizing volumes of the hippocampus and its subfields is more appropriate for this kind of issue? # Really sorry for bothering you. Thank you always for your kind and delicate solutions ! : )

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Re: [Freesurfer] FreeSurfer v5.1
by fsbuild 13 Aug '20

13 Aug '20

External Email - Use Caution Hello Jessica, I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives.  That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window. You can see the wiki page here for the 5.3 setup, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 It looks like the message indicates it is looking for ".license.txt" and not "license.txt" So in a terminal window you could try the following. First make sure FREESURFER_HOME is set, $ echo $FREESURFER_HOME /Applications/freesurfer Then take the  "license.txt" file that was emailed to you  and copy it into $FREESURFER_HOME, e..g. $ cp -p -f license.txt $FREESURFER_HOME/. Now also make a copy of it there as ".license" - no harm in having it named both ways under $FREESURFER_HOME $ cd $FREESURFER_HOME $ cp -p -f license.txt  .license.txt .... then try running things again. - R. Hua, Jessica August 12, 2020 at 17:13         External Email - Use Caution         Hi FreeSurfer, I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue: ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.   If you are outside the NMR-Martinos Center,   go to http://surfer.nmr.mgh.harvard.edu to   get a valid license file (it's free).   If you are inside the NMR-Martinos Center,   make sure to source the standard environment. I went online and filled out information to get a license.  I then added the license.txt file to the Applications/freesurfer folder, but I am still getting the same error message.  How do I get a .license file? I checked to unhide hidden files, and there is no .license file.. Jessica From: Hua, Jessica Sent: Wednesday, August 12, 2020 12:36 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: FreeSurfer v5.1   Hi FreeSurfer, To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac.  Do you know where I can find the link to install v5.1? Best, Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Hua, Jessica August 12, 2020 at 15:36         External Email - Use Caution         Hi FreeSurfer, To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac.  Do you know where I can find the link to install v5.1? Best, Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer v5.1
by Hua, Jessica 12 Aug '20

12 Aug '20

External Email - Use Caution Hi FreeSurfer, To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1? Best, Jessica Hua

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hippocampal subfields error
by Courtney Haswell 12 Aug '20

12 Aug '20

External Email - Use Caution We are getting an error after running the hippocampal subfields pipeline that we have never received before. It is happening for all subjects. We run recon-all and then the hippocampal pipeline and the output files are not being created. Below is the beginning of the log and it seems like the relevant part is "This file does not contain MRI parameters" when referring to the imageDump file. I was able to open that file and it seems ok. What could be the problem? Thank you! #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib: Warning: application is running on a locale different from the original platform locale. Warning: No display specified. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG This file does not contain MRI parameters $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/…'. ..

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Local GI error with Matlab
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 12 Aug '20

12 Aug '20

External Email - Use Caution Dear Freesurfer experts, Hope you are all safe and well. I changed the version of the matlab that I was using (from 2020a to 2019b) and most errors that I was having were fixed after running the LGI command. The only issue that I'm still having is the following (see below) - does anyone know how I could fix this? Thank you! < M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 6 (9.7.0.1434023) 64-bit (maci64) July 15, 2020 For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com. >> Warning: Argument must be a string scalar or character vector. > In ver (line 45) In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26) Error using fprintf Function is not defined for 'struct' inputs. Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15)); Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); >> ERROR: find_corresponding_center_FSformat did not complete successfully!

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Hippocampal subfields --> normalization
by Haewon Roh 12 Aug '20

12 Aug '20

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Comparing surface maps
by Fotiadis, Panagiotis 11 Aug '20

11 Aug '20

External Email - Use Caution Hello FS experts, I have a cohort of subjects for whom I created cortical thickness and T1w/T2w signal ratio surface maps, projected them to fsaverage’s surface, smoothed them, and then created average thickness and T1w/T2w maps using mris_preproc. Is there a way to statistically compare the two averaged surface maps (i.e., come up with a third surface map displaying correlation patterns between thickness and T1w/T2w signal across the surface)? Thanks in advance! Best, Panos

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Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors
by Angel Hammond 11 Aug '20

11 Aug '20

External Email - Use Caution Hello Freesurfer Experts, I wanted to re-post a portion of a question that a previous team member posted on June 20th, 2019 (See: Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors) We have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across a few cases that had questionable segmentation. The T1s had were processed using FS 5.3, and we used the command "segmentHA_T1.sh" from the latest Dev version. -We have come across about 5 subjects' medical nuclei masks that are located in the Putamen region (more superior/detached from the rest of the amygdala) on one side of the brain (in some cases just the right side, in other cases just the left side). In all of the other subjects, we don't see that same detached looking segmentation into the putamen on one side as these few show. I will attach screenshots to show this. -I have checked the aseg for these subjects as suggested in the previous question, and the hippocampus, amygdala, and putamen all look fine there. I have also checked the output volumes for the medial nucleus of these subjects and the numbers all look fine. -So, my main question is: If the placement of the medial nucleus is wrong in the segmentation (detached/in the putamen as shown) but the aseg looks correct, can we still use those values reliably? Thank you! Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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