[Freesurfer] Running MATLAB on a MAC PRO

External Email - Use Caution Hi All : I just bought a 2023 MAC PRO with an M2 Ultra Chip for my lab. It's running macOS Ventura. I have installed MATLAB on it but it refuses to run in a terminal or from the Applications folder. MATLAB runs perfectly fine on my other Linux

Re: [Freesurfer] Recon-all completed without error in 10 seconds

External Email - Use Caution Hello Lauren: Open the sR0391178-0002-1-000208-01.nii.gz file using freeview and see if the whole 3D brain is in place. This should give you a clue as to why this occurred. best, Alan On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens wrote: >

Re: [Freesurfer] T2 FLAIR Images

new surfaces. For example: > > > > recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 > > “ > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu&g

Re: [Freesurfer] T2 FLAIR Images

the --flair flag is slotted? thanks, Alan On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve wrote: > External Email - Use Caution > > Sorry, you need to pass it to recon-all with --flair or --T2 > > On 8/21/2023 1:19 PM, Alan Francis wrote: > > External Ema

Re: [Freesurfer] T2 FLAIR Images

l register them together. Or do > you just want to register them outside of recon-all? > > On 8/14/2023 2:46 PM, Alan Francis wrote: > > External Email - Use Caution > Good evening Doug et all: > > I am trying to coregister T1 and T2 images and run the recons. How

[Freesurfer] T2 FLAIR Images

External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same

[Freesurfer] T2 FLAIR images

External Email - Use Caution Good evening all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/

[Freesurfer] MAC OS Ventura problems

External Email - Use Caution Hi Doug et al, I recently moved from Linux to MAC OS running Ventura. When I run the recon-all, it gives me this message: “mri_compute_overlap” cannot be opened because the developer cannot be verified. The help given at the FS website is for

Re: [Freesurfer] Tracula statistics outputs for version 7.2

to correct for b0 inhomogeneity distortions you need to > provide the PE direction of your volumes. > > Best, > > Chiara > > > > On Jul 18, 2023, at 1:01 PM, Alan Francis > wrote: > > > > External Email - Use Caution > > > > > >

Re: [Freesurfer] Tracula statistics outputs for version 7.2

ome/alanfrancis/IMAGING/DTI/109123/109123_7T_DWI_dir72_AP_SBRef.nii.gz > > Best, > > King-Wai > > On Tue, Jul 18, 2023 at 12:59 PM Alan Francis > wrote: > >> Hi King-Wai: >> >> I have been running Tracula on 7T images and it keeps giving me an error. >> The error i

Re: [Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi King-Wai: I have been running Tracula on 7T images and it keeps giving me an error. The error is as follows: copernicus:~/IMAGING/DTI> trac-all -prep -c dmrirc-109123_7T_2 Unmatched '"'. I have attached my config file. Can you please let me know

Re: [Freesurfer] Thalamic segmentation error

to > install the Matlab runtime environment, > > $ cd $FREESURFER_HOME/bin > $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b > > - R. > > On Oct 19, 2022, at 16:41, Alan Francis wrote: > > External Email - Use Caution > > Hi Eugenio - >

Re: [Freesurfer] Thalamic segmentation error

-web.cisco.com/1-F2deM4oNalZVW-blsG0oWLgbKUPi9lklFoUJexQqa87w6TBW80F65uV3keXC_JNnhNLjdgs5T3DVG3xGEMIgcb7cMHk2Q_ALBFO9Oi6RrXZyCulsv9K8E_IWAPqNCnI1vFAlkCEf71E98zI0kcYlNH6bHeV9q3ASpBGrbdZM55ULbrYFlerLR3edJIPeSOZkReV7GSq0OlTnO8h6R0G38zKEZdDh-2r98CGtXw-xmmNTNyKlT9K-tpnOb9wFWu5viucqTNIlnzPhcp5yWDmDwUuQyb8g50ui9YFgpCNoMSrr0WMSkbg9zqr7LxhdyS4/http%3A%2F%2Fwww.jeiglesias.com > > > On Oct 18, 2022, at 2:37 PM, Alan Francis &g

[Freesurfer] Thalamic segmentation error

External Email - Use Caution Hi Eugenio - Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help. Thanks, Alan copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770

Re: [Freesurfer] Tracula - Preproc

re > # cd ANTs > # git checkout v2.3.1 > # cd - > > # If you want to build a particular release, do so here > cd ANTs > git checkout v2.3.1 > cd - > > you can also try v2.3.5 or v2.4.0. > > I don't know if it will work or not because I don't write this script. >

Re: [Freesurfer] Tracula - Preproc

Use Caution > > Hi Alan, > > Do you have the latest version of ANTs? > It should be 2.1.0 > Older version don't have all the binaries and scripts required by trac-all. > > Best, > > King-Wai > > On Mon, Aug 15, 2022 at 11:49 AM Alan Francis > wrote: > >&g

Re: [Freesurfer] Tracula - Preproc

, 2022 at 10:13 AM Alan Francis wrote: > Thank you so much King Wai, > > On Fri, Aug 12, 2022 at 5:12 PM King-Wai Chu > wrote: > >> External Email - Use Caution >> >> For bash shell >> ANTSPATH=/home/afrancis/Imaging/ANTs >> >> For

Re: [Freesurfer] Tracula - Preproc

aging/ANTs > > On Fri, Aug 12, 2022 at 5:54 PM Alan Francis > wrote: > >> External Email - Use Caution >> >> Hi Anastasia : >> >> I installed ANTS and tried this >> >> set ANTSPATH = /home/afrancis/Imaging/ANTs >> >> but it did

Re: [Freesurfer] Tracula - Preproc

NTs for registration, you have to have ANTs installed > and set ANTSPATH to its location. > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> >

Re: [Freesurfer] Tracula - Preproc

u don't get all these, your FSL is not installed correctly. > > Best, > > King-Wai > > On Fri, Aug 12, 2022 at 12:34 PM Alan Francis > wrote: > >> External Email - Use Caution >> >> Hi Anastasia and King wei - >> >> I checked the d

Re: [Freesurfer] Tracula - Preproc

rom FSL. It's needs to be in $FSLDIR. > -- > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> > *Sent:* Thursday, August 11, 2022 3:30 PM &g

[Freesurfer] Tracula - Preproc

External Email - Use Caution Hi Anastasia, King Wei: I did as you suggested with the config file and the preprocessing ran for a bit but then an error occurred. I have attached the run script. It says BET not found. Is this the Brain Extraction tool? Could you please shed some

Re: [Freesurfer] Tracula Config file.

e. > Change ac to acomm and you should be good to go. > > Best, > > King-Wai > > On Fri, Aug 5, 2022 at 4:23 PM Alan Francis > wrote: > > External Email - Use Caution > > Hi King-Wai - > > First of all, thank you so much for taking the time to invest

Re: [Freesurfer] Tracula Config file.

Chu wrote: > External Email - Use Caution > > Hi Alan, > > They still don't match. > See attached excel file. > > Best, > > King-Wai > > On Fri, Aug 5, 2022 at 2:35 PM Alan Francis > wrote: > >> External Email - Use Cautio

Re: [Freesurfer] Tracula Config file.

) don't match. > You have more than 3 paths in the pathlist and only 3 numbers in ncpts. > > Best, > > King-Wai > > > > > On Fri, Aug 5, 2022 at 10:53 AM Alan Francis > wrote: > >> External Email - Use Caution >> >> Good morning Anast

Re: [Freesurfer] Tracula Config file.

than 3 paths in the pathlist and only 3 numbers in ncpts. > > Best, > > King-Wai > > > > > On Fri, Aug 5, 2022 at 10:53 AM Alan Francis > wrote: > >> External Email - Use Caution >> >> Good morning Anastasia - >> >> I made the chang

Re: [Freesurfer] Tracula Config file.

t; names and they're not going to work. You want your RC file to have the > minimum necessary for your analysis. > > Best, > Anastasia. > > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu&g

Re: [Freesurfer] Tracula Config file.

-- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> > *Sent:* Thursday, August 4, 2022 12:23 PM > *To:* Freesurfer > *Subject:* [Freesurfer] Tracula Config file. > > >

[Freesurfer] Tracula Config file.

External Email - Use Caution Hi Anastasia - Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " " I have attached the RC file. Could you

[Freesurfer] Periaqueductal gray (PAG) volume

External Email - Use Caution Hi Doug et al, I know that this question may have been asked before, but does the latest version of FS segment/ parcellate the volume of the periaqueductal gray (PAG? Thank you, Alan --

[Freesurfer] Tracula on a stand alone workstation

External Email - Use Caution Hi Anastasia - Is it possible to run Tracula on a stand alone Linux machine (Ubuntu) which has 64 GB RAM and hyper threading? At Martinos, I used to run this on the cluster. Thanks, Alan --

[Freesurfer] (no subject)

External Email - Use Caution Hi Eugenio - Hope you are well. I am trying to extract the HSF from a group of processed brains. Previously I used the command: quantifyHippocampalSubfields.sh 195950 HSF_Cannabis Has this changed? If so what is the new command? Thanks, Alan --

Re: [Freesurfer] Tracula question

number of volumes in your DWI data. I think it's > expecting to find a b=0 volume as the 64th volume, but your DWI nifti has > only 63 volumes. > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.

[Freesurfer] Tracula question

External Email - Use Caution Dear Anastasia - I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this? Thank you, Alan [airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is

Re: [Freesurfer] TrackVis question

e the gradients extracted from the data by FSL (or > freesurfer). > > Ruopeng > > On May 23, 2019, at 5:02 PM, Alan Francis > wrote: > > External Email - Use Caution > > Hi Ruopeng - > > I used Diffusion Toolkit to recon DTI data that was preprocessed using &g

[Freesurfer] aparcstats2table

External Email - Use Caution Hi Doug: I used the following command: [airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects 100610 --hemi rh --meas thickness --tablefile aparc_stats.txt However, I got an error message: File

Re: [Freesurfer] Choroid plexus analysis

External Email - Use Caution Hi Ben - Although I have not worked on this myself, it is my belief that FS quantifies the CP fairly accurately. The volumes of the CP are being used in understanding etiology and pathogenesis of psychiatric disorders such as Schizophrenia. The lab I

Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions

External Email - Use Caution Hi Kody - In my view, its best not to do group comparisons using data from scanners of different field strengths. Even between scanners of same magnetic field strength (e,g., 3T Siemens and 3T GE), there are large variations that need to be covaried

Re: [Freesurfer] Cortical White matter/corpus callisum

the corpus? > > My understanding is that the volume of the corpus is included in the > calculation of the volume of the cerebral white matter. > > Can you confirm? > > Thank you, > > Elisabetta > > > > > > -- > *From:* freesurfer-boun...@

Re: [Freesurfer] Cortical White matter/corpus callisum

Hello Elisabetta - The Corpus callosal volumes are included in the ASEG output and not in the WM files. They are titled CC_Anterior, CC_Midbody etc. Best, Alan On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta < elisabetta_de...@hms.harvard.edu> wrote: > Dear experts, > Is the corpus

Re: [Freesurfer] Matlab 2016b and localGI

Hi Jennifer - Ostensibly your pathways and environment variables look correct. I ran into this problem once before, so I changed from BASH to the enhanced C shell and it worked. You may want to try that. All you need to do is to exit out of bash and set the environment in tcsh and it could work.

Re: [Freesurfer] quantifyHippocampalSubfields.sh

gt; ERC Senior Research Fellow > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 22 Nov 2016, at 18:00, Alan Francis <alandarkene...@gmail.com> wrote: > > Hi Eugenio - > > The command I use

Re: [Freesurfer] quantifyHippocampalSubfields.sh

of any subject > you’ve analyzed? > Cheers, > /Eugenio > > Juan Eugenio Iglesias > ERC Senior Research Fellow > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 22 Nov 2016, at 16:48, Alan Fr

[Freesurfer] quantifyHippocampalSubfields.sh

Hi Eugenio - Hope all is well with you at UCL. I have the run the subfields algorithm on a set of subjects using Freesurfer 6.0. All the brains were processed without much fuss. However, when I ran the following: quantifyHippocampalSubfields.sh DM_125 Cannabis_HSF.txt It yielded nothing. Can

Re: [Freesurfer] Repost: Error using LGI script despite making suggested chages to Matlab script.

Hi Prasser: Did you set the environment for MATLAB e.g., setenv MATLABPATH /Applications/MATLAB_versionsetenv PATH ${MATLABPATH}/bin:${PATH} This is required for FS to source MATLAB. best, Alan On Thu, Sep 29, 2016 at 6:46 PM, prasser wrote: > Hi, Reposting. Thanks. > >

Re: [Freesurfer] LGI and MATLAB

Thanks Bruce. On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> 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

[Freesurfer] LGI and MATLAB

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 getting an error. Is there any way to overcome this? Thanks, Alan afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer

[Freesurfer] LGI problem

Hi Marie: I am trying to run the LGI algorithm on 32 brains. As shown in the archives, I set the environment (on tcsh) and provided the MATLAB pathway. [afrancis-mac:~] afrancis% setenv MATLABPATH /Applications/MATLAB_R2015a.app/ [afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH}

Re: [Freesurfer] Tract length

ing into > question their utility (see Wang et al., 2012; doi: > 10.1016/j.neuroimage.2011.12.062). However, tract volume at least makes > more intuitive sense (for example, quantifying Wallerian degeneration in T1 > scans is essentially a volume measure). I thought Alan raised an importan

Re: [Freesurfer] TRACULA

I file is. I am not sure why Tracula > cannot open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is > where the the dti file is. > > > On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis <alandarkene...@gmail.com> > wrote: > >> Hi Jasmin - >> >>

Re: [Freesurfer] TRACULA

1:55:16 mreuter Exp $ > > reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz... > > Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue > Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tu

Re: [Freesurfer] TRACULA

Hi Jasmin - In your dmrirc file , the dcmlist refers to the dicom list. You have put the BVEC/BVAL files there. That is not correct. You need to place the actual pathway to your niftis in this position. set subjlist = (40 39 36) # Input diffusion DICOMs (file names relative to dcmroot) # If

Re: [Freesurfer] FreeSurfer 6.0

ly within a week or so > > On Wed, 16 Mar 2016, Alan Francis wrote: > > Hi Elizabeth: >> >> I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. >> Beta is available for download. Here is the URL: >> >> https://surfer.nmr.mgh.harvard.edu/

Re: [Freesurfer] FreeSurfer 6.0

Hi Elizabeth: I ran the Hippocampal subfields on 6.0 beta. The parcellation looks great. Beta is available for download. Here is the URL: https://surfer.nmr.mgh.harvard.edu/fswiki/Download best, Alan On Wed, Mar 16, 2016 at 6:23 AM, Elisabeth Paul < elisabeth.p...@student.uva.nl> wrote: >

Re: [Freesurfer] FreeSurfer 6.0

l-disclaimer > >> > >> - Original Message - > >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > >> Sent: Wednesday, March 16, 2016 3:

Re: [Freesurfer] DTI - Tracula question

table and >> b-value table as separate files. >> >> Run "mri_convert --help" to see all image file formats that we can >> handle. >> >> Hope this helps, >> a.y >> >> On Wed, 3 Feb 2016, Alan Francis wrote: >> >

Re: [Freesurfer] DTI - Tracula question

6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis < > alandarkene...@gmail.com> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Friday, February 5, 2016 at 3:57 PM

Re: [Freesurfer] DTI - Tracula question

pass those volumes to TRACULA, and pass the gradient table > and b-value table as separate files. > > Run "mri_convert --help" to see all image file formats that we can handle. > > Hope this helps, > a.y > > > On Wed, 3 Feb 2016, Alan Francis wrote: > > Hi Anastasi

Re: [Freesurfer] (no subject)

Hello Achcha: Detailed instructions on how to install FS on Windows via Virtual Box can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage best, Alan On Fri, Jan 22, 2016 at 3:28 PM, Ачча Чимагомедова wrote: > > Hello! > > My name

[Freesurfer] DTI - Tracula question

Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to

Re: [Freesurfer] HSF in 5.3

w.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > -- > *From: *"Alan Francis" <alandarkene...@gmail.com> > *To: *"Eugenio Iglesias" <e.igles...@bcbl.eu> > *Cc: *"Freesurfer

Re: [Freesurfer] HSF in 5.3

1 Nicotine_HSF.txt > > Let me know if it doesn't work! > > Cheers, > > /Eugenio > > > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-discla

Re: [Freesurfer] HSF in 5.3

legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > -- > *From: *"Alan Francis" <alandarkene...@gmail.com> > *To: *"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, > "eiglesias" <eigles...@bcbl.eu&

Re: [Freesurfer] Hippocampal subfields

ffusion), then you need to look into the mgz segmentation > files. > Cheers > Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > &g

[Freesurfer] Hippocampal subfields

Hi Eugenio: Hope all is well. I have a question. I have run the HSF algorithm on 32 brains and they ran smoothly without problems. I used only T1 scans. I did not have T2s. Now to extract the data, do I need to run the following: *.FSspace.mgz*: the additional scan, rigidly registered to the T1

Re: [Freesurfer] HSF in 5.3

6.0 is released, which should be pretty > soon=. > Cheers, > Eugenio > > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > --

Re: [Freesurfer] Trackvis/ Diffusion Toolkit

enerated tracks, they looked weirdly straight. I have a hunch that I am processing 'already processed' brains and hence this anomaly. Please advice. Thanks, Alan On Thu, Nov 12, 2015 at 4:20 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > Hi Alan, > > The tracks loo

[Freesurfer] Trackvis/ DTK Tracula question

Hi Anastasia: I processed 42 brains on Tracula and it ran without problems. I am now trying to run them individually on DTK to test another hypothesis. [I am using the DTK for the first time]. I loaded the diffusion weighted image, filled the parameters in the GUI and ran one single brain.

[Freesurfer] LGI processing problem

Hi Marie: I installed the Image Processing Toolbox on Matlab 2015a and proceeded with the analysis of brain that underwent the recon- all processing. However, it gave me another error message which is as follows. Could you please help me. thank you, Alan Hi Marie: I just had another problem

Re: [Freesurfer] LGI problem

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Thu, Apr 30, 2015 at 2:29 PM, Alan Francis alandarkene...@gmail.com wrote: Thank you Marie. I believe that it indeed the problem. best, Alan On Thu, Apr 30, 2015 at 12:21 PM, Marie Schaer marie.sch

[Freesurfer] LGI problem

Hi Marie: I am trying to run the LGI post processing step on 60 ASD subjects. I am using FreeSurfer 5.3. The recons went well and the processed brains look great. However when I run the LGI step, I am getting the following error which is as follows: Could you please help me? [alanf@micc

[Freesurfer] Tracula data and ICV

Dear Anastasia: Hope all is well. I have done tracula analysis on 75 brains (HARDI) and I am statistically analyzing the data. Do I need to use ICV as a covariate in my statistical model? thank you, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD*

Re: [Freesurfer] Trac -all error

will not be able to complete TRACULA processing without it You have to make sure your freesurfer recon is there, or define SUBJECTS_DIR appropriately if it's elsewhere. Hope this helps, a.y On Thu, 26 Feb 2015, Alan Francis wrote: Hi Anastasia: Sorry to bother you again. I ran trac all

Re: [Freesurfer] trac all -p

and dcmlist. a.y On Wed, 25 Feb 2015, Alan Francis wrote: Hi Anastasia: I have run trac-all using the following command: trac-all -prep -c /data/alanf/FreeSurfer_5.3/ diffusion_recons/dmrirc-101309 However, I get an error message which is as follows: INFO: SUBJECTS_DIR is /data/alanf

[Freesurfer] Trac -all error

Hi Anastasia: Sorry to bother you again. I ran trac all on our cluster but it gave me an error message. I have enclosed the text file. I used vim to see if I could decipher the error but I am not entirely sure what the problem is Please advice. thanks, Alan trac-all.o103866 Description:

[Freesurfer] trac all -p

Hi Anastasia: I have run trac-all using the following command: trac-all -prep -c /data/alanf/FreeSurfer_5.3/diffusion_recons/dmrirc-101309 However, I get an error message which is as follows: INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3/diffusion_recons INFO: Diffusion root is

Re: [Freesurfer] Gyrification index vs cortical surface area

Hi Knut: Gryification and Surface Area are two completely different things. Surface Area, as measured by FreeSurfer, gives you the area of the surface (roughly length x breadth) of a given region of interest: e.g., Pars triangularis. It is measured in millimeter squared. Gyrfication index, by

Re: [Freesurfer] prefrontal gyrification

HI Melly: I assume that you have run your brains through the FreeSurfer recons. Once you have done this and made corrections to the surfaces, run your brains through a post processing step as below: recon-all -s subj -localGI This will give you gyrification indices for all lobes across the

Re: [Freesurfer] Tools for FreeSurfer group analysis in R

Hi Andreas: Very kind of you to share your code. I am sure many of us will benefit from this. thanks, Alan Francis On Mon, Jul 21, 2014 at 9:12 AM, Andreas Berger n0642...@students.meduniwien.ac.at wrote: Hello FreeSurfers, during the course of my diploma thesis i wrote a few R functions

Re: [Freesurfer] Cerebellar Vermis

: http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm best, Alan Francis On Tue, Jul 15, 2014 at 8:53 AM, Sarosh, Cyrus csar...@med.umich.edu wrote: We are interested in using the Cerebellar vermis for an analysis with our PET data. Is the cerebellar vermis segmented during the FreeSurfer

[Freesurfer] LGI error

Hi Marie FreeSurfers: I am running the LGI command on a group of brains and I am getting an error message. MATLAB opens up and begins to run when this error appears: M A T L A B (R) Copyright 1984-2011 The MathWorks, Inc.

Re: [Freesurfer] LGI error

On Jul 9, 2014, at 11:51 AM, Alan Francis alandarkene...@gmail.com wrote: Hi Marie FreeSurfers: I am running the LGI command on a group of brains and I am getting an error message. MATLAB opens up and begins to run when this error appears: M A T L A B (R

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

. Lee Doctoral Candidate Department of Psychology Center for Mind and Brain University of California, Davis On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis alandarkene...@gmail.com wrote: Hi Bruce and FreeSurfers: I have received a manuscript to review for possible publication

Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

to segment the subfields. Joshua - Joshua K. Lee Doctoral Candidate Department of Psychology Center for Mind and Brain University of California, Davis On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis alandarkene...@gmail.comwrote: Hi Bruce and FreeSurfers: I have received

[Freesurfer] Hippocampal subfields on 1.5 Tesla

can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

[Freesurfer] Subfields on 1.5 Tesla

only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

Re: [Freesurfer] BVECS and BVALS file

this helps, a.y On Mon, 17 Feb 2014, Alan Francis wrote: Hi Anastasia: Yes I am using a standard MGH diffusion sequence. thanks, Alan On Fri, Feb 14, 2014 at 10:20 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - The gradient table is not saved in the nifti

Re: [Freesurfer] BVECS and BVALS file

On Fri, 14 Feb 2014, Alan Francis wrote: Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header

[Freesurfer] BVECS and BVALS file

Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these

[Freesurfer] kvl quantify script

elsewhere? thanks so much, Alan Francis Martinos Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] kvl quantify script

, Alan Francis wrote: Hi Eugenio; I ran the kvl quantify script for 70 processed Asperger brains. However, it was not able to save the output since the the nmr center disallows folks from saving data in the pathway /usr/local/freesurfer/stable_5_3/data is there anyway I can modify

Re: [Freesurfer] kvl quantify script

Iglesias igles...@nmr.mgh.harvard.edu wrote: Hi again, Alan, can you please send me the exact command you are running, as well as the value of SUBJECTS_DIR, FREESURFER_HOME, and so on? Cheers, /E On Fri, 2014-02-07 at 14:46 -0500, Alan Francis wrote: Hi Eugenio: Thanks

[Freesurfer] Hippocampal subfields script.

Hi Eugenio: I have HSF data on 60 Asperger brains. Is there a script that will allow me to extract the volumes into a single location? thanks so much, Alan Francis Martinos Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Hippocampal subfields script.

/HippocampalSubfieldSegmentation Cheers, /E On Mon, 2014-02-03 at 14:52 -0500, Alan Francis wrote: Hi Eugenio: I have HSF data on 60 Asperger brains. Is there a script that will allow me to extract the volumes into a single location? thanks so much, Alan Francis Martinos Center

Re: [Freesurfer] Freeview question

Thanks Bruce. On Fri, Dec 6, 2013 at 2:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Alan yes, this one: https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf although it is based on the CMA manual definitions cheers Bruce On Fri, 6 Dec 2013, Alan Francis

[Freesurfer] Freeview question

Hi Bruce et al, Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a brain in Freeview? thanks, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Linux recon-all error

Hi Krista: You may want to update tcsh. You can do this by using SUDO and 'yum update'. best, Alan On Thu, Nov 14, 2013 at 10:42 AM, krista kelly krista.kell...@gmail.comwrote: Hello, I'm running freesurfer's recon-all using Linux and the past few subjects I've run, recon-all has exited

[Freesurfer] Cerebellar subdivisions

Hi Bruce et al, Is the parcellation of the cerebellar subdivisions in the works for the next version of FS? Is there an ETA for this? thanks so much, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Tracula and Qdec

Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan

Re: [Freesurfer] Tracula and Qdec

Hi Anastasia: I am looking at Average AD in these tracts. thanks, Alan On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Alan - Are you looking at average AD over the whole tract, or AD along the tract? a.y On Fri, 13 Sep 2013, Alan Francis

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