Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30064 discussions

Error in mris_anatomical_stats
by stdp82＠virgilio.it 26 Sep '17

26 Sep '17

Hi list,using FS-FAST I have obtained a map reporting - Red_positive cluster shows difference for FC of group A > FC of group B- Blue_negative cluster shows difference for FC of group B < FC of group A Because I would like to extract the value of cortical thickness from each cluster, I have saved using tksurfer the ROI.label of each cluster (Red_positive.label and Blue_negative.label) Please note that each cluster was thresholded + 1.3 Red_positive.label - 1.3 Blue_negative.label Next, I have extracted the thickness of each cluster.Thus, I have used:mri_label2label --srcsubject Subj01 --srclabel ROI.label --trgsubject Subj01 --trglabel Subj01/label/ROI.label --hemi lh --regmethod surfaceandmris_anatomical_stats -l Subj01/label/ROI.label -b Subj01 When applied the mri_anatomical_stats to blu cluster (Blue_negative.label), this error occurs: mris_anatomical_stats -l Subj01/ROI_neg.label -b Subj01 lh limiting computations to label /Subj01/label/ROI_neg.label.reading volume Subj01/mri/wm.mgz...reading input surface Subj01/surf/lh.white...Using TH3 vertex volume calcTotal face volume 211969Total vertex volume 209028 (mask=0)reading input pial surface Subj01/surf/lh.pial...reading input white surface Subj01/surf/lh.white...No such file or directorymris_anatomical_stats: could not open label file Subj01/label/ROI_neg.labelNo such file or directorySubj01: could not read label file Subj01/label/ROI_neg.label Thanks Stefano

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Re: [Freesurfer] bad midline cut
by Antonin Skoch 26 Sep '17

26 Sep '17

Dear Bruce, Gabor, while reading this thread, I think that there is misunderstanding. -noaseg flag of recon-all indeed disables using aseg.presurf, whereas -autorecon2-noaseg does the same thing as -autorecon2-cp (at least in dev version, looking at the recon-all code). Antonin Skoch Hi Gabor you don't want to specify -noaseg. That tells recon-all not to use the aseg. I think autorecon2-cp and autorecon3 should do the trick cheers Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > Dear Bruce, > > I've corrected the lateral ventricles in the aseg.presurf.mgz and ran "recon-all -autorecon2-noaseg > -autorecon3 -subjid". Although the labels in aseg.mgz is fine the surfaces (and midline cut) > remained bad. Any other idea how to correct this type of error? > > Best Regards, > Gabor > >

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Saving individual labels from aseg
by Fereshte 26 Sep '17

26 Sep '17

Dear Experts, Is it possible to convert aseg file to individual lables ( except the one introduced by Jared Tanner) ? Thank you!

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Automatic Topology Correction
by Fereshte 26 Sep '17

26 Sep '17

Dear FreeSurfer Developers Is it possible to correct topological defects automatically in FreeSurfer? ( not correcting manually with Recon Edit) Thank you.

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Re: [Freesurfer] Freesurfer Digest, Vol 163, Issue 45
by Kartik Naik 26 Sep '17

26 Sep '17

Subject: Brain MRI Data sets. Dear Experts, I am a student of final year engineering.I am working on the project for Brain tumour detection.for which i need Mri image datasets, can anyone help me out to get those MRI scans. Looking forward for your support in this field.Thanking you. Sincerely yours. Kartik Naik On Tue, Sep 26, 2017 at 9:30 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. generating automatic functional label (Yagmur Ozdemir 19) > 2. Re: Error in segmentHA_T1 (Iglesias Gonzalez, Eugenio) > 3. Re: Problem with New Hippocampus/Amygdala Segmentation > (Iglesias Gonzalez, Eugenio) > 4. Fwd: longtitudinal pipeline (miracle ozzoude) > 5. mne_surf2bem error persists after editing file in freeview > (Anna Kasdan) > 6. Re: mne_surf2bem error persists after editing file in > freeview (Bruce Fischl) > 7. Re: generating automatic functional label (Douglas N Greve) > 8. Re: Fw: sim-sign abs/ cluster summary results confirmation > (Douglas N Greve) > 9. Re: Automatic Topology Correction (Fereshte) > 10. Volume Version of ?h.sphere.reg and method to read it > (Daniel van de Velden) > 11. Re: Automatic Topology Correction (Bruce Fischl) > 12. Re: bad midline cut (Gabor Perlaki) > 13. Re: Volume Version of ?h.sphere.reg and method to read it > (Bruce Fischl) > 14. Re: bad midline cut (Bruce Fischl) > 15. freesurfer longitudinal pipeline (miracle ozzoude) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Sep 2017 19:21:03 +0000 > From: Yagmur Ozdemir 19 <yozdemir19(a)amherst.edu> > Subject: [Freesurfer] generating automatic functional label > To: Freesurfer support list ?[freesurfer(a)nmr.mgh.harvard.edu]? > <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <4C60F8ADC8518344A2F46EEE28EA3380D4DF554E@EX10-MC1-NODE01. > amherst.edu> > Content-Type: text/plain; charset="windows-1256" > > Hello FreeSurfer developers, > > This is a piece of code I came across for producing a functional label > with using time course estimates from MEG/EEG data, for freesurfer use. I > am wondering if something similar is available to estimate a functional > label/region from fMRI data with similar tresholding. > > https://martinos.org/mne/stable/auto_examples/inverse/ > plot_label_from_stc.html#generate-a-functional-label-from-source-estimates > > Best, > Idil >

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PySurfer 0.8.0 release
by Eric Larson 26 Sep '17

26 Sep '17

Dear All, We are pleased to announce the 0.8.0 release of PySurfer, a Python-based package for visualizing Freesurfer data. This release includes bugfixes and multiple enhancements, including: - The surface geometry that is displayed can now be changed after initializing a Brain instance with e.g. brain.set_surf("smoothwm"). - Allow using custom matplotlib colormap objects or the names of custom colormaps that have been registered with matplotlib. - Added four new colormaps from seaborn: rocket, mako, icefire, and vlag. - Terrain interaction is now possible via the ``interaction`` keyword argument. - An API reference page is now available. - Support is now provided for visualizing vector-valued (3 values per vertex) data. Please see our website (http://pysurfer.github.io/) for information on installation, documentation, and the example gallery. We hope you find it useful in your research! Eric Larson, Michael Waskom, Alexandre Gramfort, and the Nipy team

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modeling thickness data at a given age
by Eryilmaz, H. Hamdi 26 Sep '17

26 Sep '17

Dear all, We are modeling changes in cortical thickness over time using a cross-sectional design. We have two groups of participants, age 8 to 18. In the cortical regions that interest us, there is generally a linear decline in thickness with age. Each group can be fitted to a best-fit line. The question we are interested in is whether there is a significant difference in thickness between groups at a given age (i.e., not just collapsed across age) — specifically, at the earliest age point (age=8). Is this possible to model across the brain surface in Freesurfer? Thanks, Hamdi and Josh

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Volume Version of ?h.sphere.reg and method to read it
by Daniel van de Velden 26 Sep '17

26 Sep '17

Dear Freesurfer Team, I am using your reconstruction pipeline for my study. Since I need to morph all my subjects to an average subject (using mne-python for this) for upcoming a Volume Source Analysis I deeply looked into the whole source-code of both software packages. Narowing down the problem, I think I will need a volume version of the ?h-sphere.reg files, which are created during the whole reconstruction process. Mne-python reads the subject specific 'sphere_tris' from this file. If I would have a similiar file for the volume edges that would be helpful. Do you agree with my conclusion and see where I am going? Thanks in advance for any kind of help. Yours sincerely, Daniel van de Velden .

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mne_surf2bem error persists after editing file in freeview
by Anna Kasdan 25 Sep '17

25 Sep '17

I am trying to create a high-resolution image to use with mne in mne_analyze. I first ran mkheadsurf -subjid s and this did not result in any errors. I then ran mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif s-head.fif and ran into an error about vertices for a few of my subjects. input file # 1 : ../surf/lh.seghead / id = 4 / sigma N/A output file : EVO07-head.fif New quad file : nvert = 288077 nquad = 294014 Triangle and vertex normals and neighboring triangles...[done] Vertex neighbors...Too many neighbors for vertex 92055. I tried editing the seghead.mgz file in freeview, and filled in the voxels that were missing at the neck. I then reran the mkheadusrf command (mkheadusrf -subjid s --noseghead), still with no errors, but got the same error as before again when I ran the mne_surf2bem command. Suggestions? Many thanks! Anna

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longtitudinal pipeline
by miracle ozzoude 25 Sep '17

25 Sep '17

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a command i can use to preform this? Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this? Thanks. Paul

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