Re: [Freesurfer] LGI label statistics

ut >> 2. add back the line w/o the # sign >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Huang, Yujing >> Sent: Friday, December 2, 2022

Re: [Freesurfer] LGI label statistics

2, 2022 10:57 AM To: Freesurfer support list Subject: Re: [Freesurfer] LGI label statistics External Email - Use Caution Thanks! As the subject ID in my example is A152 should this be replaced by $subj in the label section too? Each individual has a label created via label2label from a

Re: [Freesurfer] LGI label statistics

d back the line w/o the # sign > > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Huang, Yujing > Sent: Friday, December 2, 2022 10:34 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] LGI label statistics > > Hi Luke, > > I don’t know any

Re: [Freesurfer] LGI label statistics

nt: Friday, December 2, 2022 10:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] LGI label statistics Hi Luke, I don’t know any bash script available to perform the batch job. You can enter it in a for loop at prompt. From your $SUBJECTS_DIR, for subj in `ls -1` do echo "mri_se

Re: [Freesurfer] LGI label statistics

ntout from the echo first before submitting the jobs. Hope this helps. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Luke K Harper Sent: Friday, December 2, 2022 10:08 AM To: Freesurfer support list Subject: Re: [Freesurfer] LGI label statistics External E

Re: [Freesurfer] LGI label statistics

External Email - Use Caution Hi Yujing Ah great, Thank you so much for your help! That was the answer. I have been able to extract the stats now using the following script: mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i $SUBJECTS_DIR/A152/surf/rh.pial_lg

Re: [Freesurfer] LGI label statistics

Hi Luke, Can you try to pass the full path to your label file? Instead of 'rh.c1.label', pass '/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label' to mri_segstats. I think that should work. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Luke K Harper Sent: Fri

Re: [Freesurfer] lGI value aberrantly high, again

.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > Von: freesurfer-boun...@nmr.mgh.harvard.edu > im Auftrag von Douglas N. Greve > > Gesendet: Mittwoch, 26. Januar 2022 23:02:04 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesur

Re: [Freesurfer] lGI value aberrantly high, again

IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve Gesendet: Mittwoch, 26. Januar 2022 23:02:04 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] lGI value aberrantly high, a

Re: [Freesurfer] lGI value aberrantly high, again

Sorry, the developer of this program has moved on in her career so we have no one to support it anymore. We maybe looking at it again in the next year or so. On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote: > External Email - Use Caution > > Dear all > > as some other posted before me, so

Re: [Freesurfer] LGI - output issue

External Email - Use Caution It worked! Thank you so much for fixing this. I am also trying to open ?h.pial-outer-smoothed file. How should I proceed with either freeview or tksurferfv? Haven't found any info regarding this on the wiki! Again, thank you so much for your help! Al

Re: [Freesurfer] LGI - output issue

This is fixed in v7.2, but if you want to patch your current freesurfer distribution, you can try these commands: cd $FREESURFER_HOME/bin sudo mv fsvglrun fsvglrun.backup sudo curl -O https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun sudo chmod +x fsvglrun best Andrew

Re: [Freesurfer] LGI - trouble creating output file for each subject

External Email - Use Caution Dear Dr. Douglas, Thank you so much for your response. I just checked in the surf folder of this specific subject and yes, rh.white does exist. Not 100% sure how to check if it's readable for freesurfer - could you please explain? Thank you! On Tue, A

Re: [Freesurfer] LGI - trouble creating output file for each subject

It says that it cannot find /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white does that file exist and readable? On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caut

Re: [Freesurfer] LGI FS 7.1

*Sent:* Sunday, June 20, 2021 10:34 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] LGI FS 7.1 The biggest changes are intensity normalization and highres support, but many more changes. See the release notes *MailScanner has detected a possible fraud attempt from "

Re: [Freesurfer] LGI FS 7.1

fer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] LGI FS 7.1 The biggest changes are intensity normalization and highres support, but many more changes. See the release notes MailScanner has detected a

Re: [Freesurfer] LGI FS 7.1

efore comparing groups. Thank you for your advise, best wishes, Elisabetta *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Sunday, June 20, 2021 10:34 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] LGI FS 7.1 The biggest changes are inte

Re: [Freesurfer] LGI FS 7.1

Douglas N. Greve Sent: Sunday, June 20, 2021 10:34 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LGI FS 7.1 The biggest changes are intensity normalization and highres support, but many more changes. See the release notes https://secure-web.cisco.com/1xB0JoEP4

Re: [Freesurfer] LGI FS 7.1

The biggest changes are intensity normalization and highres support, but many more changes. See the release notes https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote: External Email - Use Caution External Email - Use Caution

Re: [Freesurfer] LGI error on FS7.1

This was fixed in 7.11. You can use that version or copy the attached file to this location $FREESURFER_HOME/matlab/freesurfer_read_surf.m On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi, I am using Matlab R2014a, and FS7.1.0 and receiving this error when I try

Re: [Freesurfer] LGI quality control {Disarmed}

When you click on the gray areas, is the value 0 or just something very close to 0? You may need to set the lower threshold (default is 2). Also, I would recommend using freeview via tksurferfv (same command line as tksurfer) On 11/4/2020 2:12 PM, Nelson, Eric wrote: External Email -

Re: [Freesurfer] LGI output question

I'm not sure what you mean by the mean area for the different LGI values. Can you elaborate? On 10/20/2020 6:46 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, I have performe

Re: [Freesurfer] LGI value extraction

That is really LGI. aparcstats2table just defaults to "thickness". But you should double check that the value you see in lh.aparc_lgi.stats is the same as in result_lgi_lh.txt On 9/29/2020 12:38 PM, 祝菲 wrote: External Email - Use Caution Dear expert, I have used freesurfer v6.0 to c

Re: [Freesurfer] lGI permutation and monte-carlo

On 6/9/2020 11:27 AM, Avi Gharehgazlou wrote: External Email - Use Caution Thank you so much for your input, it was very helpful and I really appreciate it. Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after co

Re: [Freesurfer] lGI permutation and monte-carlo

External Email - Use Caution Thank you so much for your input, it was very helpful and I really appreciate it. Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after correcting for multiple comparisons using monte-

Re: [Freesurfer] lGI permutation and monte-carlo

On 6/8/2020 8:12 PM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, Upon reading your 2018 paper (cited below) and following threads on the archives, I am aware that I should use permutation testing for lGI analyses rather than monte carlo at p<0.05. However, I ha

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I had the identical problem (failure at segmentation stage, as described below) in 4 subjects of my dataset. I have no possibility to run analyses on a linux machine… Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi doug, I tried to re-run 3 or 4 times and always failed at the segmentation stage… I have no linux machine, but I can try in a mac computer with a different OS... thank you! Angela > Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve > ha s

Re: [Freesurfer] LGI problem

Hi Angela, I cannot replicate this error. If you re-run, does it always exit with error? You can try this quickly be running setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen cd /Users/angelafavaro/Desktop/Aachen/subj220/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/a

Re: [Freesurfer] LGI problem

External Email - Use Caution I have uploaded to you the data using the Martinos Center FileDrop Hope is a good option for you Thank you Angela > Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro > ha scritto: > > External Email - Use Caution > > > Hi Doug,

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug, I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working... I am trying to overcom

Re: [Freesurfer] LGI problem

Hmmm, I don't know. Can you upload the data set? Follow these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log  into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name:

Re: [Freesurfer] LGI problem

Someone just pointed out that I posted the wrong file. Here is the correct one. Copy it to the same folder https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m On 5/13/2020 11:01 PM, Douglas N. Greve wrote: Download this file https://gate.nmr.mgh.harvard.edu/safelinks/gr

Re: [Freesurfer] LGI problem

Download this file https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m and copy it into $FREESURFER_HOME/matlab and rerun. Let me know if that fixes it. On 5/13/2020 5:57 PM, Angela Favaro wrote: External Email - Use Caution Please find attached the

Re: [Freesurfer] LGI problem

Are you running this from recon-all? If so send the recon-all.log. If from the command line, send the command-line and all terminal output On 5/13/2020 5:28 PM, Angela Favaro wrote: External Email - Use Caution Hi Doug! yes, it run under version 6! Please let me know if it is somethin

Re: [Freesurfer] LGI problem

External Email - Use Caution Hi Doug! yes, it run under version 6! Please let me know if it is something that can be solved Thank you Angela > Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve > ha scritto: > > Does it run under version 6? We are not really supporting lG

Re: [Freesurfer] LGI problem

Does it run under version 6? We are not really supporting lGI anymore, but maybe we can get it to work On 5/13/2020 4:24 PM, Angela Favaro wrote: External Email - Use Caution Hi all, I am using the new version of Freesurfer 7.1.0 And I am finding problems in running gyrification anal

Re: [Freesurfer] LGI in QDEC menu please respond soon

harehgazlou > *Sent: *Tuesday, April 23, 2019 2:27 PM > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] LGI in QDEC menu please respond soon > > > > *External Email - Use Caution* > > Where should I type "ctrl +H"? In my linux terminal (in QDE

Re: [Freesurfer] LGI in QDEC menu please respond soon

see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.   Sent from Mail for Windows 10   From: Avi Gharehgazlou Sent: Tuesday, April 23, 2019 1:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon   External Email - Use Caution

Re: [Freesurfer] LGI in QDEC menu please respond soon

23, 2019 2:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon External Email - Use Caution Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when I do that it gives this error: bash: ctrl + H: command not f

Re: [Freesurfer] LGI in QDEC menu please respond soon

pial_lgi into .Qdecrc file. > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Avi Gharehgazlou > *Sent: *Tuesday, April 23, 2019 1:34 PM > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

: Freesurfer support list Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon External Email - Use Caution Yes I did On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi wrote: External Email - Use Caution Did you run this command “recon-all -s my_subject_id -qcache

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution Yes I did On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi wrote: > External Email - Use Caution > > Did you run this command “recon-all -s my_subject_id -qcache -measure > pial_lgi” before？ If not， you should run this. > > > > Sent from Mail

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution Did you run this command “recon-all -s my_subject_id -qcache -measure pial_lgi” before？ If not， you should run this. Sent from Mail for Windows 10 From: Avi Gharehgazlou Sent: Tuesday, April 23, 2019 12:06 PM To: Freesurfer support list Subject: [Fre

Re: [Freesurfer] LGI in QDEC

Hi Zheng, qdec is not longer being supported. Use the "command line" stream, see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 3/12/19 7:47 AM, 郑凤莲 wrote: > > External Email - Use Caution > > Hi experts, > I am using qdec software for the statistic of LGI. I

Re: [Freesurfer] LGI index error

External Email - Use Caution We had the same problem. This is related to a "security" feature Apple introduced some years ago, called "System Integrity Protection". Turn it off and you will be fine. Basically follow these instructions from Apple: https://developer.apple.com/

Re: [Freesurfer] LGI index error

External Email - Use Caution > Dear Freesurfer expert > > I am trying to compute LGI with Mac OS. I am a beginner of FS. > I could connect free surfer to Matlab path, but when I run LGI it generate > this error that i can not understand > > mris_fill -c -r 1 lh.pial > /Applic

Re: [Freesurfer] LGI without Matlab license?

I have not tried to compile it, sorry. On 09/06/2018 03:45 PM, Thomas, Adam (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > We’d like to calculate the Local Gyrification Index (LGI) on several > thousand scans, but our HPC cluster does not have the necessary Matlab > licenses

Re: [Freesurfer] LGI without Matlab license?

The Mathworks offers runtime distribution that contains the libraries you can build your code against w/o needing a Matlab license; you just cannot re-distirbute the files from the distribution w/o permission from The Mathworks. I’ve used it to build code that links against libmat etc. You ca

Re: [Freesurfer] LGI trouble with Matlab

External Email - Use Caution Hi, probably you need to add MATLAB path to Freesurfer's $PATH variable. The following link may help: http://www.manuelschutze.com/?p=297 On 18 May 2018 at 12:02, subin oh wrote: > External Email - Use Caution > > Hello, > > I downloaded

Re: [Freesurfer] LGI for the lobar annotation

External Email - Use Caution Thank you!! :D On Thu, Apr 19, 2018 at 12:57 PM Douglas N. Greve wrote: > yes > > > On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > > Douglas, thank you very much again. > > So I can assume it is the lGI for the area (in this case the l

Re: [Freesurfer] LGI for the lobar annotation

yes On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote: > Douglas, thank you very much again. > So I can assume it is the lGI for the area (in this case the lobe)? > > Thank you again! > > On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve > wrote: > > The

Re: [Freesurfer] LGI for the lobar annotation

Douglas, thank you very much again. So I can assume it is the lGI for the area (in this case the lobe)? Thank you again! On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve wrote: > The "intensity" is the mean value of the input (lh.pial_lgi in this case) > averaged over vertices. If you wan the to

Re: [Freesurfer] LGI for the lobar annotation

The "intensity" is the mean value of the input (lh.pial_lgi in this case) averaged over vertices. If  you wan the total number, multiply it by the number of vertices or re-run with --accumulate. The area is the surface area of the entire lobe. On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes

Re: [Freesurfer] LGI for the lobar annotation

Sorry, my mistake. mri_segstats --annot DA011 lh lobesStrict --i DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve wrote: > What is your command line? Also, please remember to post to the list > > > On 04/18/2018 02:10 PM, Fernanda

Re: [Freesurfer] LGI for the lobar annotation

What is your command line? Also, please remember to post to the list On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote: > Dear Douglas, > > thank you. > >  The code worked, but I didn't understand the result very well. What > means intensity? The area, is the ara from the piall_lgi surf

Re: [Freesurfer] LGI for the lobar annotation

Thank you, Douglas, do you have any suggestions on how to make you work? Fernanda On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve wrote: > that should work, except the command line is not quite right > > On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote: > > Good night, > > does anyone kn

Re: [Freesurfer] LGI for the lobar annotation

that should work, except the command line is not quite right On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote: Good night, does anyone know if it is possible to calculate the lGI for the ?h.lobesStrict.annot? And if it yes, how can I do it? I've already tried to use: /mri_segstats --

Re: [Freesurfer] LGI ERROR

Hi Greve, Thanks for your help. It is that I only use FWMH = 5 to do my study, it is decided by my data. Can I think it so? Sincerely, Zheng At 2017-12-14 00:06:39, "Douglas Greve" wrote: The FWHM used in the MC simulation is computed from the data itself. The final FWHM is a m

Re: [Freesurfer] LGI ERROR

The FWHM used in the MC simulation is computed from the data itself. The final FWHM is a mixture of the applied FWHM and smoothness inherent in the data. LGI has a lot of inherent smoothness, so the final FWHM is very large. The MC sim table only goes up to 30mm, after that it generates an erro

Re: [Freesurfer] LGI

Hi Greve, Thank you very much. I have another question about the whole brain volume. I want to compare the relation between age and the volume of the whole brain, total GM and total WM. I don't know where the whole brain volume is in aseg.stats. Is it segmentation brain volume? Sincerely,

Re: [Freesurfer] LGI

yes, that should work too On 11/26/17 8:38 PM, 郑凤莲 wrote: Hi Greve,     Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_*lgi* --sum lh.aparc.pial_*lgi*.stats" and get a stats file. In this file, I can get mean value unde

Re: [Freesurfer] LGI

Hi Greve, Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats" and get a stats file. In this file, I can get mean value under the "Mean" volume. Is this the same as you say? Thanks a lot !

Re: [Freesurfer] LGI

use something like cd subject/surf mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.lgi.stats -t lh.lgi.mgh -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh white In the output, the mean LGI will be under the "ThickAvg" column On 11/

Re: [Freesurfer] lGI mris_fill Error

Thank you so much for this suggestion. It worked perfectly. I really appreciate all of your help- with this and the previous question. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical Scho

Re: [Freesurfer] lGI mris_fill Error

Hi Arkadiy, This might have to do with SIP, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ Andrew On Oct 27, 2017, at 2:13 PM, Maksimovskiy, Ark

Re: [Freesurfer] lgi vertex coordinate problem

No, I am working with MATLAB on the outputs of freesurfer and the freesurfer_surf2voxels command is under MATLAB. I want to check the coordinates of lgi values found by recon - all lgi command on MATLAB. When I check the coordinates on the brain image I realize a shift app 5-10 vox according to re

Re: [Freesurfer] lgi vertex coordinate problem

I don't think that freesurfer_surf2voxles is our command is it? In any event, I don't know what you mean about shifts. On 05/19/2017 09:01 AM, Serian doma wrote: > Hi there, > > I am trying to use local gyrification index values for the purpose of > adaptive smoothing. I use recon -all and calc

Re: [Freesurfer] LGI data for each region?

Dear Shane, use this command: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats Look at the info on FreeSurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI Antonin Skoch Hi Freesurfer, How can I get the LGI meas

Re: [Freesurfer] LGI error/Matlab/ a qestion for Douglas Greve

I think the ismac.m script was introduced in later versions of matlab. You can just create your own with the following content: function y=ismac y=0; return On 02/15/2017 01:59 PM, aral ahmadi wrote: > From: Douglas N Greve > So ismac.m is not defined in your matlab implementation? What vers

Re: [Freesurfer] LGI issue/Error

So ismac.m is not defined in your matlab implementation? What version of matlab are you using? What kind of computer are you running on? On 02/02/2017 01:48 PM, aral ahmadi wrote: > > Dear experts > > I have a question regarding Freesurfer- LGI error I got during running > LGI after all recon s

Re: [Freesurfer] LGI and MATLAB

Thanks Bruce. On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl wrote: > Hi Alan > > make sure matlab is in your path. You can check by typing: > > > which matlab > > > cheers > Bruce > > On Fri, 16 Sep 2016, Alan Francis wrote: > > Hi Marie - >> >> I have MATLAB and the Image processing toolbox on

Re: [Freesurfer] LGI and MATLAB

Hi Alan make sure matlab is in your path. You can check by typing: which matlab cheers Bruce On Fri, 16 Sep 2016, Alan Francis wrote: Hi Marie - I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am

Re: [Freesurfer] LGI

I have the very same problem! Hope to be able to solve it with the guidance from Freesurfer. Best Regards, Mahtab. Friday, July 8, 2016, 01:43 +0100 from walidyassi...@gmail.com : >Hello, > >Sorry for raising this questions again. I posted this questions a while ago >(Twice), but i haven't

Re: [Freesurfer] LGI

Hello, Sorry for raising this questions again. I posted this questions a while ago (Twice), but i haven't gotten an answer yet. Can i at least know if i can tweak something for this to work? or just give up? I tried downgrading Xquatrz, to 2.7.8, but it still doesn't work! My matlab is 2016a, coul

Re: [Freesurfer] LGI Summary Statistics

It is not the same. You would have to weight by the number of vertices. You can also run mris_anatomical_stats passing the ?h.cortex.label as the label and the lgi overlay as the input On 07/06/2016 02:57 PM, Timothy Hendrickson wrote: > Freesurfer Support, > > I have seen previous message threa

Re: [Freesurfer] lGI value is aberrantly high

Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution suggested by Marie Schaer to rereconstruct The images with "randomness" Recon-al

Re: [Freesurfer] LGI problem

Hi Marie: I just had another problem with the LGI processing. Here is the log: thanks, Alan [alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-

Re: [Freesurfer] LGI problem

Hi Alan, Do you have the image processing toolbox installed in matlab? If not, I guess this is the source of the error. Best, Marie On Apr 30, 2015, at 7:51 AM, Alan Francis mailto:alandarkene...@gmail.com>> wrote: Hi Marie: I am trying to run the LGI post processing step on 60 ASD subject

Re: [Freesurfer] lGI ?h.pial-outer-smoothed

To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Tuesday 3 March 2015 21:00 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] lGI ?h.pial-outer-smoothed Hi Giedre, Small intersections like that are fine and won't affec

Re: [Freesurfer] lGI ?h.pial-outer-smoothed

Hi Giedre, Small intersections like that are fine and won't affect the lGI computation, so you are good with that. Values around 20 are however more preoccupying! Can you send me a screenshot of the lGI overlaid on the surface for this subject using tksurfer or freeview? Best, Marie NB: if

Re: [Freesurfer] LGI fails for fsaverage

That is not what Bruce is suggesting. Try to register the post-op to the pre-op using bbregister. You can then map the pre-op surfaces to the post-op brain On 10/29/2014 01:58 PM, Pierre Mégevand wrote: > Unfortunately, our pre-implant MR was acquired with double-dose > gadolinium and we can't

Re: [Freesurfer] LGI fails for fsaverage

Unfortunately, our pre-implant MR was acquired with double-dose gadolinium and we can't seem to extract the pial surface from it. have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre M?gevand wrote: > Our usual method for electrode localiz

Re: [Freesurfer] LGI analysis of single subject

Hi Maria, I have to say that I rarely use freeview, I prefer tkmedit and tksurfer that I know better. So I didn't realize that the images were shifted, I guess it's some preference in how to read the surface. I just tried and have the same kind of shift when using freeview, so I don't think yo

Re: [Freesurfer] LGI analysis of single subject

Hi Marie - Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful! I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding comma

Re: [Freesurfer] LGI fails for fsaverage

have you tried using bbregister to register post-op MRI with the pre-op surfaces? On Wed, 29 Oct 2014, Pierre Mégevand wrote: Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electro

Re: [Freesurfer] LGI fails for fsaverage

Our usual method for electrode localization remains in the patient's space: co-register post-op MR and CT with pre-op MR brainmask (our reference space) and snap electrodes to patient's outer pial surface. My idea was: register the patient's (crappy) brainmask volume to the "Talairach" fsaverage v

Re: [Freesurfer] LGI fails for fsaverage

So what I don't get in your pipeline is how you'll register the post-op brain to fsaverage if you don't have any cortical surface in the post-op? If I were you, if you want precise registration that includes the sulci, I'd go with the white surface from the pre-op gadolinium scan. And if you ju

Re: [Freesurfer] LGI fails for fsaverage

You're right, we can't use the post-op surface because of the deformation caused by surgery and the electrode artifacts. Getting a surface right from the brainmask would be OK, if we can't get anything better, but the nice thing about using the fsaverage surface is that you can plot and compare el

Re: [Freesurfer] LGI fails for fsaverage

Hi Pierre, Tricky question. So you can't really use the post-op cortical surface for this participant, right? Otherwise I would simply use the outer smoothed pial for this subject directly, which would be much more similar to the pre-op than the outer surface from the fsaverage (?). Otherwise,

Re: [Freesurfer] LGI fails for fsaverage

Thanks Marie. Here is what I'm trying to do. In fact, all I need from LGI are the first few steps, until ?h.pial-outer-smoothed has been generated. I'm not actually interested in the local GI for fsaverage. Our intra-cranial electrode localization method relies on post-implant CT and MRI scans to

Re: [Freesurfer] LGI fails for fsaverage

It does not surprise me that it fails on the fsaverage surface. I agree with Marie that it is not good idea to use LGI on fsaverage for anything. Definitely not its intended purpose. doug On 10/28/2014 03:06 PM, Marie Schaer wrote: > > Hi Pierre, > > I'm not sure exactly what you are trying to

Re: [Freesurfer] LGI fails for fsaverage

Hi Pierre, I'm not sure exactly what you are trying to do, but it's true that LGI fails for fsaverage at the mris_fills step, where the volume looks "cut". It seems to be something in the properties of the fsaverage surfaces. Maybe Doug or Bruce have an idea where it comes from. But in any ca

Re: [Freesurfer] lgi mris_preproc

you should be able to use mris_preproc On 10/9/14 1:08 PM, Lars M. Rimol wrote: Hi, In the wiki page on the gyrification index it says that to sample the results to ico, use recon-all -s my_subject_id -qcache -measure pial_lgi If I prefer not to use qudec, can I instead use mris_preproc to d

Re: [Freesurfer] LGI Topological Defect

Hi Tara try: recon-all -s -randomness -all Jon From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tara Miskovich Sent: Friday, August 22, 2014 12:07 PM To: Freesurfer support list Subject: [Freesurfer] LGI Topological Defect Hi all, I am gett

Re: [Freesurfer] LGI Topological Defect

Hi Tara, Did you try to run the recon-all with the randomness flag? If you don't add this flag, your surfaces will not change much with the new recon-all and you'll probably get the same problem again when running LGI. Let me know if you still have trouble, Marie On Aug 22, 2014, at 7:07 PM

Re: [Freesurfer] lgi for longitudinal scans

Hi Anna, that was not my suggestion, I suggested to pass both the cross sectional time point ID and the base id (together with the long flag) and additionally the -localGI flag. So if you time point 1 is XXX_1 and time point 2 is XXX_2 and your base is XXX_base then recon-all -long XXX_1 XXX_

Re: [Freesurfer] lgi for longitudinal scans

hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s? What I did (according to your suggestion) recon-all -long XXX_1.long XXX_2.long -localGI This did not work? Do you know why potentially? On Wed, Mar 26, 2014 at 3:

Re: [Freesurfer] LGI error

Thanks so much Marie. I will check the toolboxes. best, Alan On Wed, Jul 9, 2014 at 2:56 PM, Marie Schaer wrote: > > Hi Alan, > > You probably don't have the matlab image processing toolbox installed. > > Let me know if you can't install it easily. > > Best, > > Marie > > On Jul 9, 2014

Re: [Freesurfer] LGI error

Hi Alan, You probably don't have the matlab image processing toolbox installed. Let me know if you can't install it easily. Best, Marie On Jul 9, 2014, at 11:51 AM, Alan Francis mailto:alandarkene...@gmail.com>> wrote: Hi Marie & FreeSurfers: I am running the LGI command on a group of bra

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