Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

TRACULA longitudinal stream: using multiple configuration files?
by j.oschwald＠psychologie.uzh.ch 25 Oct '16

25 Oct '16

Hi Freesurfer users I wonder wether it makes a difference when using longitudinal TRACULA if all timepoints are run within one process (1 configuration file including all three timepoints) or if it is possible to split it into several independent processes (with several different configuration files - one per time point)? Thank you for your help. Jessica

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3D Mesh of hemispheric surfaces does not match space of acquisition sequence
by Conrad Christoffer Prillwitz 25 Oct '16

25 Oct '16

Dear Freesurfer-Expert, We are currently trying to develop a 3D-Model from MRI data using combined files from Freesurfer and FSL. For this purpose we run recon-all on our subject and furthermore get some ROIs from FSL-based scripts. When visualizing the Freesurfer surfaces together with the FSL ROIs in any 3D modelling software (like e.g. Meshlab or 3D Slicer), there seems to be a space mismatch meaning: the FSL-based ROIs lie more inferior relative to the Freesurfer surfaces than they should (a shift in any other direction might be there but is at least not visible by eye; see attached screenshot). If we further add a single 2D slice of the original T1.mgz file to the 3D model, it seems to be consistent with the spatial position of the FSL ROIs, while the Freesurfer surfaces are clearly shifted (at least in z-direction; see attached screenshot). However opening the surfaces and the T1.mgz in freeview instead of 3D-Slicer, the spatial position fits. Do you have any idea of why this is the case or even more important, how to bring both structures in the same "space"? As we need to continue modelling in 3D-Slicer, we are looking for a way to correct the spatial shift independent of freeview. We are very thankful for any input on this matter! Best regards, Bastian David Bastian David, M.Sc. Ph.D. candidate .............................................................. Department of Epileptology University of Bonn .............................................................. Sigmund-Freud-Str. 25 53127 Bonn .............................................................. bastian.david(a)ukb.uni-bonn.de www.epileptologie-bonn.de

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Group analysis in repeated measures anova
by Greenberg, Jonathan 25 Oct '16

25 Oct '16

Dear Freesurfer users I am trying to examine differences between 3 groups in surface thickness and volume over three time periods (pre-intervention, post-intervention, and 6-month followup). Previously, when only the first 2 time points were available, I followed the instructions for paired analysis detailed in https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. In the FSGD file, Group was the only Class. Now that I have 3 time points, I am trying to follow the instructions for repeated measures anova detailed in https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. The FSGD file structure in this case is different, with each single participant having their own Class (i.e. in my case – 60 Classes for the 60 participants), and 2 variables contrasting the time points GroupDescriptorFile 1 Class Subject1 Class Subject2 Class Subject3 Variables TP1-vs-TP2 TP1-vs-TP3 Input subject1-tp1 Subject1 1 1 Input subject1-tp2 Subject1 -1 0 Input subject1-tp3 Subject1 0 -1 Input subject2-tp1 Subject2 1 1 Input subject2-tp2 Subject2 -1 0 Input subject2-tp3 Subject2 0 -1 Input subject3-tp1 Subject3 1 1 Input subject3-tp2 Subject3 -1 0 Input subject3-tp3 Subject3 0 -1 In this case – the design matrix is (Sub1) (Sub2) (Sub3) (V1) (v2) 1 0 0 1 1 1 0 0 -1 0 1 0 0 0 -1 0 1 0 1 1 0 1 0 -1 0 0 1 0 0 -1 0 0 1 1 1 0 0 1 -1 0 0 0 1 0 -1 My question is whether and how can I incorporate participants' group (a between-subject variable) into this FSGD file? Should 3 additional Classes simply be added, one for each group, thereby making the new FSGD file as follows GroupDescriptorFile 1 Class Group1 Class Group2 Class Group3 Class Subject1 Class Subject2 Class Subject3 Variables TP1-vs-TP2 TP1-vs-TP3 Input subject1-tp1 Subject1 Group3 1 1 Input subject1-tp2 Subject1 Group3 -1 0 Input subject1-tp3 Subject1 Group3 0 -1 Input subject2-tp1 Subject2 Group2 1 1 Input subject2-tp2 Subject2 Group2 -1 0 Input subject2-tp3 Subject2 Group2 0 -1 Input subject3-tp1 Subject3 Group3 1 1 Input subject3-tp2 Subject3 Group3 -1 0 Input subject3-tp3 Subject3 Group3 0 -1 and the matrix design as follows? (Group1)(Group2)(Group3)(Sub1)(Sub2) (Sub3) (V1) (v2) 0 0 1 1 0 0 1 1 0 0 1 1 0 0 -1 0 0 0 1 1 0 0 0 -1 0 1 0 0 1 0 1 1 0 1 0 0 1 0 -1 0 0 1 0 0 1 0 0 -1 0 0 1 0 0 1 1 1 0 0 1 0 0 1 -1 0 0 0 1 0 0 1 0 -1 Thank you Jonathan

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difficulty opening fsdir on freesurfer linux
by miracle ozzoude 25 Oct '16

25 Oct '16

Hello Freesurfer team, I am having difficulty opening the fsdir folder on freesurfer linux version (linux-centos_x86_64-stable-pub-v5.3.0). First, I preprocessed it using the command "recon-all -all -i s fsdir" to get the fsdir folder and it finished without errors. However, when I tried loading the fsdir folder " cd path directory/fsdir, next freeview" the program opened without the subject's fsdir folder (i.e., blank). Please do you know how I can fix it? I never had such problem with freesurfer mac version. Thanks. Best, Paul

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Re: [Freesurfer] White matter surface don't change after editing
by Cong 24 Oct '16

24 Oct '16

Hi Dear Bruce I have uploaded a subject named Cong2Bruce.zip through ftp. I can’t fix it by myself. Could you help me how to use expert options to get correct white matter and gray matter surface. Thank you very much. Best Wished Cong Chen > Date: Tue, 20 Sep 2016 10:45:30 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] White matter surface don't change after > editing > > Hi Cong > > we are experiencing serious disk problems at Martinos, so the ftp site is > down. > > Try changing the values for mri_segment also. Note that what you are > seeing are NOT topological defects as mris_make_surfaces preserves the > input topology whatever its settings. Make sure to look in 3D and scoll > through your slices. You can also try changing the gm thresholds > > cheers > Bruce > > On Tue, 20 Sep 2016, Cong wrote: > >> Hi Dear Bruce >> ? ? ?Thanks very much for your reply, I ?improved min_border_white to >> 100, the lh.white line shrinks but still is far out in some area, ?and >> I notice many topological defect appears as a result. >> ? ? ?I failed to upload subject through ftp, it's always appear an >> error called "550 Failed to change directory", so I send a subject to >> you through FileDrop. Can you receive a file named Cong2Bruce.zip?? >> >> ? ? ?Thanks again for your help. >> >> Best Wishes >> Cong Chen >> >> Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT) >> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Cong >> >> you could try using expert options to modify the >> mris_make_surfaces? >> parameters. It looks like you white surface is too far out. Try? >> increasing min_border_white and/or increasing max_gray. If you >> can't get it? >> working feel free to upload the entire subject dir and we will >> take a look >> >> cheers >> Bruce >> >> >> On Thu, 8 Sep 2016, Cong wrote: >> >> Hi dear all >> ? ? I attach a new picture to illustrate this problem. ?I erased >> some voxels in wm.mgz and rerun. The lh.orig(blue line) looks >> well, but lh.white(yellow line) don?t along the white surface in >> some area. Could anyone give me some advice? Thanks very much. >> >> Best wishes >> Cong Chen >> >> >> Date: Sun, 4 Sep 2016 15:15:42 +0800 >> From: Cong <3110103623(a)zju.edu.cn> >> Subject: [Freesurfer] White matter surface don't change after >> editing >> >> Dear freesurfer team? >> ?I have some MRI images from a GE scanner, ?it seems that >> images? quality is poor because grey matter is bright in so much >> area and these grey matter is included in wm.mgz. So I deleted >> wrong voxels in wm.mgz by freeview and rerun through command ? >> recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But >> ?h.white (yellow line) don?t change after rerunning as you can >> see in the attached picture. ?Is this problem caused by deleting >> too many voxels and how to fix it? ?Thanks very much. >> >> Regards >> Cong Chen

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PET PVC - CSF estimation
by Adam Martersteck 24 Oct '16

24 Oct '16

Hi FreeSurfer team, Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016). 1) Is the choroid plexus included in the binarized then 3mm eroded segmentation to find the mean ventricular CSF signal? 2) Is there a way to input my own estimation of ventricular CSF signal to mri_gtmpvc? Thanks! Adam

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subject directory error: can't find subject
by Russ, Brian (NIH/NIMH) [E] 24 Oct '16

24 Oct '16

Hi, I’m attempting to use FreeSurfer to create a set of surface and flat maps for use with some macaque data. Using a number of programs prior to FreeSurfer I have created a skull-stripped T1 image and White Matter mask and then successfully used FreeSurfers mksubjdirs, mri_convert, mri_fill, etc, through to mris_inflate to create a set of surfaces. After taking a break from the data I’ve come back to it to try and convert the surface maps into flattened maps. However, tksurfer is not recognizing the subjects directory. Error: cannot find subject {subject} in ./{subject} input: setenv SUBJECTS_DIR ./ && tksurfer {subject} rh inflated I can’t seem to find anyway to make FreeSurfer reindex the subject directory without running recon-all, which I don’t want to do as I had to manually edit the masks as this is a macaque data set, and the current surfaces are quite good. Freesurfer version: free surfer-Linux v5.3.0 any help would be greatly appreciated. Brian

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question about thalamus
by Dorsa Haji Ghaffari 24 Oct '16

24 Oct '16

Hi, I have done the sub-cortical segmentation in Freesurfer and have extracted the left thalamus, when I put it on top of the original MRI, it seems like it is getting out of the border of thalamus, also it is not smooth. I wanted to ask if anyone knows how to limit the computation only to thalamus, and also make it trace the thalamus more accurately? Thank you Dorsa

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Manual pial and white matter corrections cause irregularities
by Cleo Vandervost 24 Oct '16

24 Oct '16

?Hello Freesurfer team, For my thesis I'm researching the differences in grey and white matter and cortical thickness between children with and without dyslexia. My supervisor advised me to manually edit the Freesurfer-generated data. I've been editing my data as follows: - adding control points to (larger) WM-areas that FS did not include - manually editing (smaller) WM-areas through recon-editing - correcting the pial surface through recon-editing After finishing and saving my edits I reran recon-all with this command: recon-all -autorecon2-cp -autorecon -subjid (subject number). When I opened my data again in Freesurfer to check my edits, I saw that there were two big problems: - 'distortions' in the pial surface - sometimes large areas of WM suddenly were excluded, even when I didn't make any edits in that area ?It makes the edited data look much worse than the original data, which is weird I suppose. I've included some pictures so you can see what I mean. - Picture (a) is the original unedited version. - Picture (b) is the edited version: control points and WM edits. You can see that there's a large area in the left hemisfere excluded from the original WM area - Picture (c) is the re-edited version of (b), control points added in that large area. This time it's included but the pial surface shows a lot of irregularities. Me and my supervisor tried a couple of times with other data, but we still had the same results. We also tried by only adding control points and editing manually, without the pial-corrections. Do you have any idea of what's going wrong in the editing proces? Thank you very much, Kind regards Cleo Vandervost 1st master speech and language therapy Katholieke Universiteit Leuven

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Using hippocampal subfields in SPM
by M.M. Craig 24 Oct '16

24 Oct '16

Hello All, I have a question about using the hippocampal subfield segmentation. I've got the subfields from the structural image using recon-all and now I want to use the subfields as ROIs in SPM. I've tried using mri_convert to convert the .mgz files to .nii. This works but it doesn't place the subfields where they should be on the brain. Is there a command to register the hippocampal subfield .mgz files to a structural image that can be used in SPM? Thanks very much for your help. Best wishes, Mike

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Freesurfer October 2016