Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Brain without skull and manual edits
by M del Mar Velasco 14 Sep '17

14 Sep '17

Dear all, I would like an accurate segmentation of the brain without skull in native space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I run recon-all again and it finished without errors. When I used to do that proccess with Freesurfer 5.1, I masked rawavg.mgz with brain.mgz to get the final segmented brain: mri_mask rawavg.mgz brain.mgz brainraw.mgz mri_convert -odt float brainraw.mgz brain.nii In that case, deleted voxels are set to background in brain.mgz (my manual changes affect to brain.mgz). Now I am using Freesurfer 6 and my manual erased voxels appears in brain.mgz (they are not black). So, what output from Freesurfer should I use to the above goal? Should I use brain.finalsurfs.mgz? Thanks you in advance M del Mar

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license error
by Ritesh Mahajan 14 Sep '17

14 Sep '17

Hello team, I created the license.txt at location FREESURFER_HOME and pasted the lines sent to me after registration. Still i find the following errors. "ERROR: FreeSurfer license file /usr/local/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" Thanks, Ritesh Mahajan

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problems with segmentHA_T1_long.sh
by Lara Foland-Ross 13 Sep '17

13 Sep '17

Hello, I ran a longitudinal analysis cortical structure in Freesurfer version 5.3. I'd now like to compute hippocampus subfields using the new beta version of the "Segmentation of hippocampal subfields and nuclei of the amygdala" tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) I'm running into several errors when running segmentHA_T1_long.sh. Upon closer inspection of the script, it's not clear to me whether this tool is compatible with scans processed in the 5.3 version of the longitudinal pipeline. Can you please confirm? Thanks, Lara

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BA Labels
by John Anderson 13 Sep '17

13 Sep '17

Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm analysis to check the difference between the two groups. I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to utilize these labels in such analysis. In this context I have two questions: 1. Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the command mri_binarize? 2. in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat values for every BA label. How can I derive similar stats from the SUV maps in the compiled file. Thanks in advance John

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Unknown regions in cortical parcellation
by Aidan Murphy 13 Sep '17

13 Sep '17

We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years. I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.

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mri_glmfit-sim over PALM
by Martin Juneja 13 Sep '17

13 Sep '17

Hi experts, To calculate simulations on LGI measures, I ran: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 But it gives error: ERROR: design matrix is not orthogonal, cannot be used with permutation. I came across a post where its mentioned that: "Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs. https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim" - Douglas N. Greve So I was wondering if I can use this program for LGI measures and run the same command, lets say this new program is: mri_glmfit-sim_new, so can I run the following command (instead of doing PALM): mri_glmfit-sim_new --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 Thanks.

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Normalizing volumes
by Alexopoulos, Dimitrios 13 Sep '17

13 Sep '17

Hi, We running FS 5.3 analyses on 2 cohorts (control vs. malnourished adolescents) and I was wonderful what FS measure would be most accurate for normalizing the volumes. (i.e total GM, total WM, suparatentorial, etc). The eTIV measures are significantly different between the cohorts. Is eTIV the best way to normalize or perhaps BrainSegVol? What FS measure gives you total brain volume? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Cluster-Defining Threshold of p=0.025
by Jahn, Andrew 13 Sep '17

13 Sep '17

Hello, Is it possible to use cluster-defining thresholds such as p = 0.025 with mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.) My design doesn't allow the use of permutations for simulating cluster sizes, so I have to use the mczsim option; however, from what I can tell it doesn't allow using any non-cached options. Thanks, -Andy

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Results display tool
by Chris Adamson 12 Sep '17

12 Sep '17

Freesurfer users, I just wanted to advertise a set of display tools that I wrote for easy display, in MATLAB, of regional stats like p-values/effect sizes/arbitrary scalars with customisable masks for aparc, dkt, aparc.a2009s. https://chrisadamsonmcri.github.io/freesurfer_statsurf_display I hope people find it useful. Chris. ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Resampling Freesurfer - Human connectome workbench
by Xavier Guell Paradis 12 Sep '17

12 Sep '17

Dear freesurfer experts, I have an overlay freesurfer file (format is .w) which corresponds to a thresholded seed-based functional connectivity surface map (group result). The .w file was generated from an SPM analysis, following the instructions described here (http://spmsurfrend.sourceforge.net/Documentation/SPM_SurfRend_Tutorial_V0.2…) I have one .w file for each cerebral hemisphere. I would like to visualize these .w maps using workbench_view, and I have tried to follow the instructions the HCP team published here (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF…) As a first step I would need to convert the .w files into .func.gii files using mris_convert. Then I would use wb_command -metric-resample, as indicated in the instructions. This does not seem to work with my .w file: 1) mris_convert myfile.w myfile.func.gii This generates myfile.func.gii, but when I use wb_command -metric-resample I get the following error: ERROR: Parse error while reading: error occurred while parsing element, line number: 1 column number: 1 2) As an alternative approach, I opened myfile.w using Tksurfer and saved the overlay (myfile.w) with .mgh format (generating a new file: "myfile.mgh"). Then I do the following: mris_convert myfile.mgh myfile.func.gii This generates the myfile.func.gii file, but when I use wb_command -metric-resample with this file I get a different error: ERROR: All data arrays (columns) in the file must have the same number of rows. The first array (column) contains 163842 rows. Array 2 contains 327680 rows. I have asked the HCP team, but they were not familiar with the .w files and suggested that I ask you instead. Thank you very much for your help, Xavier.

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