Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

Compile problems
by Aziz Nanthaamornphong 28 Sep '17

28 Sep '17

Hi Freesurfer experts, I ran the commands to build Freesurfer (Yosemite based) by following this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page However, I got the error message when I ran *`make install'* command as follows: gunzip: can't stat: ../../distribution/average/cvs_avg35.tar.gz (../../distribution/average/cvs_avg35.tar.gz.gz): No such file or directory mv ../../distribution/average/cvs_avg35 \ /Users/azizn/fs_install_2/subjects mv: rename ../../distribution/average/cvs_avg35 to /Users/azizn/fs_install_2/subjects/cvs_avg35: No such file or directory make[2]: *** [install] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [install-recursive] Error 1 Please let me know how to solve this problem. I need to compile the Freesurfer on my own Macbook. Best Wishes, Aziz

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Build Freeview on macOS
by Aziz Nanthaamornphong 28 Sep '17

28 Sep '17

Hi Freesurfer experts, Based on this link https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page, it mentions that "*As of the writing of this document (June 2016) freeview is unable to build on macOS 10.11 platforms and higher (El Capitan and higher)." * Could we build Freeview on macOS now? Best wishes, Aziz.

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freesurfer longitudinal pipeline
by miracle ozzoude 28 Sep '17

28 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 1001_Baseline.long.longbase and 1001_Followup.long.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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Re: [Freesurfer] bad midline cut
by Antonin Skoch 27 Sep '17

27 Sep '17

Bruce, Gabor, may I ask, does it ever matter where the midline surface lies? I thought that this does not affect anything in the analysis. Antonin hmmm, if you tar, gzip and upload the subject I'll take a look. Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote: > I've already corrected aseg.presurf.mgz and the left and right lateral ventricles are now correct in > the final aseg.mgz. However the pial surface is almost the same as earlier: > > https://mega.nz/#!XAZkWLZa!a6NgkEtiHzEqUkhZ6WimPgUKxytsGHKrgOLfyHdUuEM > > https://mega.nz/#!XRRHna7Q!vaeSLG5Cv-fGW-0xdEJlgFTNRPm7qGHOlShYh7y5z1g > >

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Freeview Versions
by Maksimovskiy, Arkadiy 27 Sep '17

27 Sep '17

Dear Freesurfer Experts, My apologies if I missed this information elsewhere on the website, but could not find any info. about it. There appear to be two Freeview versions, both from 2017 (released one day apart), for which the screenshots are attached. I was wondering if you could let me know what the difference is between the two. I do use one of them on the cluster and one locally- might that account for the difference in versions? If there are other processing differences that I should be aware of, please let me know. Thank you for all of your help and information. - Arkadiy [cid:image001.png@01D33153.34FF4EB0]

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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!

2 1

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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Freesurfer September 2017