Freesurfer

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5 participants
30076 discussions

Use CA and other subfields as seed for FS-FAST
by stdp82＠virgilio.it 03 Jan '17

03 Jan '17

Hi list, I would like to obtain the functional connectivity maps of CA1, CA2/3... by using FS-FAST (VERSION 5.3). Which are the codes in FreeSurferColorLUT.txt, that I should use, please? The ranges from 500 - 508 and from 550 - 558 are useful by using 5.3? Thanks Kind regards, Stefano Delli Pizzi

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Re: [Freesurfer] creating labels from aseg.mgz
by Ladan Shahshahani 02 Jan '17

02 Jan '17

Hi, Thanks for the reply.

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Volume-based group analysis
by Hao wen 02 Jan '17

02 Jan '17

Hello: I want to do some volume-based group analysis with Freesurfer mri_glmfit, and I know in Qdec, this has not been implemented, the problem here is very simple: I want to do the regression between the sub-cortical structure voxels number and age, so try to find the correlation significance between age and subcortical structure in aseg.stats, from the tutorial of command-line of FS from here: it is important to realize that most of the concepts learned here apply to any group analysis in FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer>, surface or volume, thickness or fMRI. So I guess I can do it, but I can not find any tutorial about this for volume-based group analysis(fMRI pipeline, I got stats from recon-all), if I use third-party software to do the statistical analysis, the difficulties are how to mapping the p-value to the brain just like VBM in SPM. Actually, this is not really different for you, but I can not just find the relevant information, can you help me??? Thanks in advance Hao

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creating labels from aseg.mgz
by Ladan Shahshahani 01 Jan '17

01 Jan '17

Dear experts, I'm trying to create labels for subcortical regions. I want to use these labels to extract time series from resting state fMRI data (I want all of the subcortical time series and I want them to be in mni305 space). I'm not sure if I'm doing the right thing. Here's an example of what I used: mri_cor2label --c $FREESURFER_HOME/subjects/fsaverage/mri.2mm/aseg.mgz --id 255 --l ~/Desktop/CC_Anterior.label After running this command, attached is the label file I get. The first column is all "-1"s. any ideas how I can go about doing such thing? Best, Ladan

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mri_glmfit-sim
by stdp82＠virgilio.it 31 Dec '16

31 Dec '16

Hi list, which is the correct option, please? 1- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .0166 --3spaces 2- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .05 --3spaces Thanks Best regards Stefano

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Revisiting GM ROI list
by P Taylor 30 Dec '16

30 Dec '16

Hi, Doug- I've looked more into my earlier question of identifying FS-returned regions, in particular: 1) which regions of the whole FreeSurferColorLUT.txt seem to get returned by default recon-all calls (for either the 2000- or 2009-parc+segs); and 2) which of those regions are GM and non-GM (WM/CSF/other), based both on the mri_binarize list you had posted earlier in this thread and on the names given in the LUT. I'd like to pick your brain on this. A) The main questions I have relate to the regions labeled from [0, 256], which seem have the same labelling in both the 2000 and 2009 parc+segs. >From a few different FreeSurfer recon-alls on healthy adults, below is a list of the ROIs that seem to be consistently returned by recon-all (a much sparser subset than all 256). For each, I have included the number and label, as well as put arrows by the numbers that, according to the MatchValues list in mri_binarize, should be in either the WM or Vent masks, (and hence non-arrowed regions should be GM, by how that function returns "--gm"). My main questions arise about #30, 62, 80 and 85, as they don't appear to be GM-- therefore, am I correct that I should also *exclude* those four regions from a list of GM regions? (Here, "FS_nongm*" means that it was in the list of non-GM regions in mri_binarize, as either unknown, WM, CSF or ventricle.) ------------------------------------------------------------ ----------------------------------------- 0 Unknown -> FS_nongm 2 Left-Cerebral-White-Matter -> FS_nongm_wm 4 Left-Lateral-Ventricle -> FS_nongm_vent 5 Left-Inf-Lat-Vent -> FS_nongm_vent 7 Left-Cerebellum-White-Matter -> FS_nongm_wm 8 Left-Cerebellum-Cortex 10 Left-Thalamus-Proper 11 Left-Caudate 12 Left-Putamen 13 Left-Pallidum 14 3rd-Ventricle -> FS_nongm_vent 15 4th-Ventricle -> FS_nongm_vent 16 Brain-Stem 17 Left-Hippocampus 18 Left-Amygdala 24 CSF -> FS_nongm_csf 26 Left-Accumbens-area 28 Left-VentralDC 30 Left-vessel -------> *should be in list of FS_nongm? 31 Left-choroid-plexus -> FS_nongm_vent 41 Right-Cerebral-White-Matter -> FS_nongm_wm 43 Right-Lateral-Ventricle -> FS_nongm_vent 44 Right-Inf-Lat-Vent -> FS_nongm_vent 46 Right-Cerebellum-White-Matter -> FS_nongm_wm 47 Right-Cerebellum-Cortex 49 Right-Thalamus-Proper 50 Right-Caudate 52 Right-Pallidum 53 Right-Hippocampus 54 Right-Amygdala 58 Right-Accumbens-area 60 Right-VentralDC 62 Right-vessel -------> *should be in list of FS_nongm? 63 Right-choroid-plexus -> FS_nongm_vent 72 5th-Ventricle -> FS_nongm_vent 77 WM-hypointensities -> FS_nongm_wm 80 non-WM-hypointensities -------> *should be in list of FS_nongm_wm? 85 Optic-Chiasm -------> *should be in list of FS_nongm? 251 CC_Posterior -> FS_nongm_wm 252 CC_Mid_Posterior -> FS_nongm_wm 253 CC_Central -> FS_nongm_wm 254 CC_Mid_Anterior -> FS_nongm_wm 255 CC_Anterior -> FS_nongm_wm ------------------------------------------------------------ -------------------- It seem that the new version of mri_binarize that you had sent me might still include those four flagged regions in the 'mri_binarize --gm' output. B) For the ROIs specific to the 2000aparc+aseg, I think it also seems pretty clear: + 1000 and 2000 are returned as "ctx_*_unknown"; + All ROIs in the intervals [1001, 1003] and [1005, 1035] can be returned, and these are all LH GM; + All ROIs in the intervals [2001, 2003] and [2005, 2035] can be returned, and these are all RH GM; + ROIs '1004' and '2004' are the "ctx-?h-corpuscallosum", which would be WM, but they don't seem to be returned. C) For the ROIs specific to 2009aparc+aseg, I think it also seems pretty clear: + 11100 and 12100 are returned as "ctx_*_Unknown"; + All ROIs in the intervals [11101, 11141] and [11143, 11175] can be returned, and these are all LH GM; + All ROIs in the intervals [12101, 12141] and [12143, 12175] can be returned, and these are all RH GM; + ROIs '11142' and '12142' are the "ctx_?h_Medial_wall", which would be non-GM, but they don't seem to be returned. D) And you mentioned that the regions in the interval [3000, 4035] are WM parcellations. So, in total, does that seem like a complete categorization of regions that are typically returned, as well as their classification as either GM or non-GM? And in particular, I would be happy to know your thoughts on the flagged ROIs in the interval [0, 256]. Thanks, pt

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Re-running recon-all in V6 {Disarmed}
by Kevin Aquino 30 Dec '16

30 Dec '16

Hi all, When V6 is released I'd want to re-run all my (10) subjects through recon-all again (they were processed with v6 alpha). I'd like to keep all my wm edits, mask and control points, is it as easy as just running recon-all on the same folder again? They are 0.7mm so I'd like to keep all the corrections. Cheers! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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under estimation of white matter and pial surface
by miracle ozzoude 29 Dec '16

29 Dec '16

Hello Freesurfer, I was wondering if anyone knows how to correct an underestimation of white matter and pial surface outputs from freesurfer. I attached an image showing the error. Thanks. Best, Paul

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Fwd: localGI bug
by David Groppe 28 Dec '16

28 Dec '16

Dear FreeSurfer Developers, I think there is a bug in FreeSurfer's MATLAB code that is used to compute the local gyrification index. Specifically, when I run this command: *recon-all -s PT001 -localGI* I get the following error: *face 115000 / 118360mesh_outer = vertices: [59182x3 double] faces: [118360x3 double] facesOfVertex: [59182x1 struct]preparing pial mesh structure ......searching for mesh edges...done (171.44 sec).... creating path file for vertex 1 / 59182area file for outer ROIs saved at 1In an assignment A(:) = B, the number of elements in A and B must be the same.Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2));Error in mesh_vertex_nearest (line 29)nearestIndex = dsearchn(vertices,points);Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);* *>> ERROR: make_roi_paths did not complete successfully!* I ran the command in debugging mode and *x* and *yi *are both empty variables. I am using a freshly installed version of the Lion OS X 10.7 (64b Intel) version of FreeSurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg; freesurfer-Darwin-lion-stable-pub-v5.3.0) and am running on OS 10.11.6 using MATLAB version R2015b (8.6.0.267246). The recon-all.log is attached. Let me know if there is any further information I can provide and thanks for producing such a fantastic piece of freeware. -David Groppe

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recon-all Line search failed
by Ladan Shahshahani 28 Dec '16

28 Dec '16

Dear experts, I tried running recon-all for a subject and it exited with the following error: LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and my operating system is 14.04.1-Ubuntu. attached is the recon-all.log. Best, Ladan

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