Re: [Freesurfer] help

Use mri_binarize --i aseg.mgz --match 17 --binval -1 --o your.lefthippo.nii.gz On 4/6/17 6:00 AM, Dilip Puri wrote: Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using

[Freesurfer] help

Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate

Re: [Freesurfer] help error RB_ALL_2008-03-26

Hi Flavia can you send us the reon-all.log and also what version you are trying to run? cheers Bruce On Wed, 22 Feb 2017, Flavia Arduini wrote: > Hi, > I try tu run this code: > recon-all -s CAROFILO -i > /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii > -autorecon2-wm

[Freesurfer] help error RB_ALL_2008-03-26

Hi, I try tu run this code: recon-all -s CAROFILO -i /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii -autorecon2-wm but compare this error ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca How can I fix this problem? Thanks Flavia Arduini

Re: [Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

Not sure. Can you upload the set to https://gate.nmr.mgh.harvard.edu/filedrop2 and I'll take a look On 01/10/2017 03:31 PM, Caleb Comoglio wrote: > Hello, > > I am having trouble with the MRI_convert portion of recon-all. I get > the error below when I run recon-all and when I run

[Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

Hello, I am having trouble with the MRI_convert portion of recon-all. I get the error below when I run recon-all and when I run MRI_convert independently of recon-all. WARNING: file Desktop/3T_20161201_131733544/MR04 does not contain a Siemens ASCII header has this file been anonymized?

Re: [Freesurfer] Help with Opseq: Setting Parameters

Not really. You can force there to always be a NULL with --tnullmin. You can also specify the maximum duration of the null event with --tnullmax; this should indirectly cause there to be more instances where nulls appear between non-nulls. On 11/21/16 1:17 PM, Leshin, Joseph wrote:

[Freesurfer] Help with Opseq: Setting Parameters

Greetings, Is it possible to avoid having Optseq repeat my events more than 3 times before inserting a NULL? In other words, I get sequences that look like ev1, ev5, ev4, ev2, ev6, NULL, etc. Ideally, I'd have Optseq limit event repetitions at 2-3 followed by a NULL. I tried using "-repvar"

[Freesurfer] Help resolving ERROR: Invalid FreeSurfer license key found in license file

Hej. I recently tried to create a license file for a Unix-based installation of FreeSurfer that previously had no license file associated with it. With the help of our IT people, I have tried copying the lines I received via email into a file named ‘license.txt’ and then following responses I

[Freesurfer] Freesurfer Help

Hello, I just downloaded and installed Freesurfer and I had just a few basic questions.  1. When I type in the command to "test the installation type" using "tksurfer bert lh inflated -annotation aparc" I get the bert brain image, however I don't get the tksurfer tools popup below it with all

[Freesurfer] Help with error in mkcontrast-sess command

Hi Freesurfers I am doing FSFAST with my own data and have a problem. After I run mkanalysis-sess command succesfully, I try to run mkcontrast-sess command but I get an error during the process. The text in my terminal window is the following: root@usuario2:/home/usuario2... mkcontrast-sess

Re: [Freesurfer] Help - Surface extraction to Matlab

Hi Ittai We distribute m-files for reading and writing. Try read_surf.m Cheers Bruce > On Feb 18, 2016, at 4:02 AM, Ittai Shamir wrote: > > Hello, > > My name is Ittai and I am currently working on my M.Sc. in the department of > Neurobiology in Tel Aviv

[Freesurfer] Help - Surface extraction to Matlab

Hello, My name is Ittai and I am currently working on my M.Sc. in the department of Neurobiology in Tel Aviv University. I am a new FreeSurfer user. My question regarding the software is- After successfully running my data (T1 image - MPRAGE) through FS, I would like to extract both cortical

Re: [Freesurfer] Help importing files from a previous SPM analysis

you have to do the whole thing On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote: > Do I have to run recon-all entirely in order to extract volume for a > few Brodmann's areas? Or is there a way of optimizing the process by > striping it of any unneeded calculations? > > It is

Re: [Freesurfer] Help importing files from a previous SPM analysis

Hi Luis sorry, the BA stuff is almost at the very end so you will need to run pretty much everything. We are down to 8 hours or so on modern multi-core CPUs (and even faster than that with 4-8 threads) cheers Bruce On Tue, 22 Dec 2015, Luis Fernado Silva Castro de Araújo wrote: Do I have

Re: [Freesurfer] Help importing files from a previous SPM analysis

Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations? It is taking 21h to analyze one subject. Best, luis 2015-12-22 9:44 GMT+11:00 Douglas N Greve

Re: [Freesurfer] Help importing files from a previous SPM analysis

Dear Douglas, It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command. If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right? Does the command

Re: [Freesurfer] Help importing files from a previous SPM analysis

If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run recon-all -s yoursubjectname -all -i inputfile inputfile can include img but be warned that img does not have information about

Re: [Freesurfer] Help importing files from a previous SPM analysis

are you doing anatomical analysis (recon-all) or functional analysis (FSFAST)? On 12/20/15 8:43 PM, Luis Fernado Silva Castro de Araújo wrote: Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too

[Freesurfer] Help importing files from a previous SPM analysis

Hi all, I am just starting to learn to analyse neuroimaging data. So these are my first steps with FreeSurfer. I apologize if the question is too basic to the mail list. I set myself the goal of finding volumes for several areas in a dataset from the lab I am working on, but I got stuck very

Re: [Freesurfer] Help with desired (sub)cortical GM thickness

Hi Daniele I guess you could play with the intensity thresholds in mris_make_surfaces, although we do try to do this in an intensity-independent manner (to first order) Bruce On Mon, 16 Nov 2015, Daniele Perrone wrote: > Hi Freesurfer Experts, > > I successfully used FreeSurfer to segment

[Freesurfer] Help with desired (sub)cortical GM thickness

Hi Freesurfer Experts, I successfully used FreeSurfer to segment (sub)cortical GM using the "recon-all" pipeline, and I am wondering now how to control the final thickness of segmented GM. In other words, for a single subject, I want to obtain GM masks and parcels that are volumetrically

Re: [Freesurfer] Help with desired (sub)cortical GM thickness

I'm not sure what you mean. Can you elaborate? doug On 11/16/2015 09:24 AM, Daniele Perrone wrote: > Hi Freesurfer Experts, > > I successfully used FreeSurfer to segment (sub)cortical GM using the > "recon-all" pipeline, and I am wondering now how to control the final > thickness of segmented

Re: [Freesurfer] Help with V6

p://www.bcbl.eu/legal-disclaimer> - Original Message - From: Noah Markowitz <noahb.markow...@gmail.com<http://gmail.com>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Sent: Sat, 04 Jul 2015 13:57:53 +0200 (C

Re: [Freesurfer] Help with recon-all

Hi Michael sure, send us the recon-all.log. We don't get many segfaults, and usually they are because you ran out of RAM or disk space. Were you running other things on the machine at the same time? We will need this info: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting cheers Bruce

[Freesurfer] Help with recon-all

Hi all, I am new to FreeSurfer, so this may be a novice question. We are running recon-all and the script finished without errors for all of our subjects except for one. I have opened the recon-all.log file to examine the output, but am not sure where to locate the error. The last thing

[Freesurfer] help with mris_make_face_parcellation

Hi, I’m interested in using mris_make_face_parcellation, but I can’t find any documentation on the input arguments and outputs. Could you give me more information on this command or direct me to the proper website? Thanks, Sophie -- Sophie Wohltjen Post-baccalaureate Fellow Laboratory of Brain

Re: [Freesurfer] Help with Freesurfer preprocessing pls

list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls no! Don't delete those files - we need them. Just don't include them in your for loop cheers Bruce On Mon, 3 Aug 2015, Lim, Lena wrote: Thanks, Bruce. So do I delete that files and run recon-all -qcache -subjid $i for all

Re: [Freesurfer] Help with Freesurfer preprocessing pls

have so far ? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:41 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls I think you

Re: [Freesurfer] Help with Freesurfer preprocessing pls

[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:04 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls no! Don't delete those files - we need them. Just don't include them in your for loop cheers Bruce On Mon, 3 Aug

Re: [Freesurfer] Help with Freesurfer preprocessing pls

Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls I think you should be all set. I meant don't delete fsaverage and all On Mon, 3 Aug 2015, Lim, Lena wrote: Sorry, I don’t understand. Those files are now in the directory. What exactly should I run next? -Original Message

Re: [Freesurfer] Help with Freesurfer preprocessing pls

...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:41 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls I think you should be all set. I meant don't delete fsaverage and all On Mon, 3 Aug 2015, Lim, Lena wrote: Sorry, I don’t

Re: [Freesurfer] Help with Freesurfer preprocessing pls

,   Lena     -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 30 July 2015 18:02 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls   Hi Lena   you

Re: [Freesurfer] Help with Freesurfer preprocessing pls

, Lena -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 30 July 2015 18:02 To: Freesurfer support list Subject: Re: [Freesurfer] Help

Re: [Freesurfer] Help with Freesurfer preprocessing pls

To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls Hi Lena those aren't files that you need to recreate - they are distributed with FS (which is also why you don't have permission to write into their directories). You should leave them out of the list that you

Re: [Freesurfer] Help with Freesurfer preprocessing pls

: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 15:38 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls Hi Lena those aren't files that you need to recreate

[Freesurfer] Help

Hi, I've been having problems with my license when I try to run the autorecon. I get this error message ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid

Re: [Freesurfer] Help

Hi Katherine you can try changing permissions on the .license file if you own it: chmod +w $FREESURFER_HOME/.license if you don't you'll have to get the owner (or a sysadmin) to change it cheers Bruce On Fri, 31 Jul 2015, Petrilli Paolino, Katherine wrote: Hi,  I've been having

Re: [Freesurfer] Help with Freesurfer preprocessing pls

Hi Lena you need to run the hippocampal subfield code. Depending on what version you are running it could mean adding something like: -hippocampal-subfields-T1/T1T2/T2 and removing the -autorecon-all cheers Bruce On Thu, 30 Jul 2015, Lim, Lena wrote: Dear Freesurfer experts,   My

Re: [Freesurfer] help with using optseq2

] Sent: Monday, July 20, 2015 1:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help with using optseq2 The problem is probably that you have specified a maximum for the null event and it just does not need as much run time (# of time points) that you have allocated. On 07/16/2015

Re: [Freesurfer] help with using optseq2

] Sent: Friday, July 17, 2015 1:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] help with using optseq2 This type of design is not suitable for optseq2. Furthermore, you only have 100s of task and almost 300s of scan time. This will lead to lots of empty space. You really need more than

Re: [Freesurfer] help on mris_preproc

: [Freesurfer] help on mris_preproc I think you have a non-standard directory structure. FS is expecting something like $SUBJECTS_DIR/subject1 but it looks like you have the FS results in $SUBJECTS_DIR/subject1/freesurfer You have to use the FS structure or else it will generate an error doug

Re: [Freesurfer] help with using optseq2

The problem is probably that you have specified a maximum for the null event and it just does not need as much run time (# of time points) that you have allocated. On 07/16/2015 06:17 PM, Heeyoung Choo wrote: Hello, I'm trying to create trial sequences for a slow event related fMRI

Re: [Freesurfer] help on mris_preproc

Sent: Monday, June 29, 2015 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: Hi Doug, Thanks. I can see that the mris_preproc command reads the header information

Re: [Freesurfer] help on mris_preproc

, June 29, 2015 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: Hi Doug, Thanks. I can see that the mris_preproc command reads the header information in register.dat. I

Re: [Freesurfer] help with using optseq2

This type of design is not suitable for optseq2. Furthermore, you only have 100s of task and almost 300s of scan time. This will lead to lots of empty space. You really need more than 2 conditions per event type. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow,

[Freesurfer] help with using optseq2

Hello, I'm trying to create trial sequences for a slow event related fMRI experiment. I have 10 classes of stimuli, and each stimulus lasts 5 sec and repeats twice in a run. Environment: Linux 3.13.0-35-generic #62-Ubuntu SMP UTC 2014 x86_64 x86_64 x86_64 GNU/Linux I ran: ./optseq2 --ntp

[Freesurfer] help

I am very new to Freesurfer and are having problems getting it up and running. I have followed, successfully the set up and configuration instructions up the license. At this point, after entering the license information received in the email I try and to exit and save and I get a message that

Re: [Freesurfer] help

As the error message indicates, this is a permissions issue. To solve the license problem, your best bet is to create the license files in your home directory (or anywhere you have adequate permissions) and copy it to /Applications/freesurfer. This is described in a little more detail in the

Re: [Freesurfer] Help with V6

-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Sat, 04 Jul 2015 13:57:53 +0200 (CEST) Subject: Re: [Freesurfer] Help with V6 Hey Eugenio, I was able to resolve it with the help of another expert

Re: [Freesurfer] Help with V6

Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help with V6 Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv

Re: [Freesurfer] Help with V6

researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 3, 2015 4:20:02 AM Subject: [Freesurfer] Help

[Freesurfer] Help with V6

Hi, I’m trying to run the ‘beta’ version of FS6, centos4, and encountered the error: ‘ERROR: Flag -hippocampal-subfields-T1 unrecognized’. I setenv and source just as described for previous versions. Also, I have Matlab 2014b downloaded on the computer (obviously comes with runtime) but am

Re: [Freesurfer] help on mris_preproc

*Subject:* Re: [Freesurfer] help on mris_preproc Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric

Re: [Freesurfer] help on mris_preproc

Sent: Friday, June 12, 2015 3:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] help on mris_preproc Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using

Re: [Freesurfer] help on mris_preproc

Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI

[Freesurfer] help on mris_preproc

Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI analyses. I encountered some issues with mris_preproc to assemble IRF results to the fsaverage surface. Please advise on how to resolve

[Freesurfer] Help FreeSurfer

Dear FreeSurfer Users, I have tried to download FreeSurfer but I am not sure I’ve done it correctly. Could you send me a guide to download it properly? Inside freesurfer there is only “Freeview” as a program. Is that correct? I notice that there is a folder “matlab”, isn’t there a description

Re: [Freesurfer] Help~ How to fix this error？ Thanks

Try increasing the memory allowed to the Virtual machine at startup. -Zeke On Apr 11, 2015, at 10:25 AM, nellie nellie_w...@163.com wrote: Hi, I’m a beginner of Freesurfer. When I tried to run the commend of “recon-all -all” with my data, the following error occurred: ...

[Freesurfer] help optseq2 question

Dear Doug Greve Hi, I am glad to write to you. I am a graduate student in Institute of Psychology, Chinese Academy of Sciences. It is my first time doing fMRI experiment. Now I meet some difficulties while using Optseq2. I hope you can help me. Thank you very much. The following are

Re: [Freesurfer] Help with optseq2

Thank you so much! That solved my issue! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 12, 2015 8:42 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help

Re: [Freesurfer] Help with optseq2

The psdwin controls the window over which HRF overlap correction needs to be done. This is usually something like 0-22 sec, enough time for the HRF to return to baseline. If you want to set the minimum/maximum ITI, then use --tnullmin and --tnullmax doug On 03/11/2015 08:08 PM, Michael T

[Freesurfer] Help with optseq2

Hi, I am getting a unexpected result when I am running optseq2 and I don’t know if it is something I am not understanding correctly or if something else is going on. It is with ITI times. If I understand correctly the psdwin I entered below should return a min time of 4 and a max of 10, but I

[Freesurfer] Help: error on running dt_recon

Dear freesurfer experts,Sorry for posting such a long message but I am trying to run dt_recon command on DTI images acquired in dicom format using 3T_Toshiba (Toshiba_MEC_MR3). Image parameters are: Scanning sequence =Spin Echo; TR=9 ; TE=082.0 ; Flip angle = 90; Slice thickness= 3.;

Re: [Freesurfer] Help: error on running dt_recon

Just give it one of the dicoms (ie, don't use the * wild card, just give it the actual file name of one of the files in the series, it will find the rest) doug On 2/11/15 4:28 PM, Sampada Sinha wrote: Dear freesurfer experts, Sorry for posting such a long message but I am trying to run

[Freesurfer] help-convert vome index to vertex numbe in surface

hello I have some points defined in volume (RAS coordination) and now I want to see these locations (vertex number) on surface. I don't know how to do it. I can see one point using tkmedit, input the coordination and save point and then in tksurfer, go to saved point, so I can get the vertex

Re: [Freesurfer] Help on DTI pre-processing

Hi Gabriel - The standard pre-processing in tracula is likely to work for all these cases. To make sure that the standard registration-based eddy-current correction worked for all cases, you should look at the final correct images (dmri/dwi.nii.gz) and make sure that all images in the series

[Freesurfer] Help on DTI pre-processing

Dear all,I have a question regarding the pre-prossesing steps of DTI data.I have 5 different datasets, each with different acquisition parameters, including the number of directions (16, 32 and 64), the b-value (1000, 1300 and 1500) and the magnetic field (1.5 and 3T). Do you think that a single

Re: [Freesurfer] Help with pial boundary

: [Freesurfer] Help with pial boundary To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.lrh.2.03.1409090827060.23...@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Joann it looks like some white matter is not being identified

Re: [Freesurfer] Help with pial boundary

Hi Joann it looks like some white matter is not being identified in the ?h.white surface. You need to diagnose why this is happening. It's probably an inaccurately corrected topological defect. Have you gone through the tutorials? You will likely need to add some wm voxels back in. If you

Re: [Freesurfer] help extracting Brodmann areas masks

Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual

Re: [Freesurfer] help extracting Brodmann areas masks

p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On

Re: [Freesurfer] help extracting Brodmann areas masks

Hi Bruce, First of all, thanks for the reply! There was a typo in my initial question, so I rewrote it to make it clearer : # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label --l lh.label --ctab

Re: [Freesurfer] help extracting Brodmann areas masks

Hi David - On the difference between .thresh and not .thresh labels: The BA labels come from averaging histologically derived labels from a set of post mortem brains. The non-thresholded version is just the sum of the corresponding labels from the different brains in fsaverage space. So

Re: [Freesurfer] help extracting Brodmann areas masks

Thanks for the reply Anastasia, that makes it more clear. I realized that I was confused due to my inexperience with freesurfer and was using the wrong approach. I did not realize I could simply use the segmented volumes in aseg.mgz corresponding to the visual cortex using

[Freesurfer] help extracting Brodmann areas masks

Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the

[Freesurfer] Help with mris_convert

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label

[Freesurfer] Help with QDEC Sig Cluster annotations and mri_convert and mri_annotation2label

Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot

Re: [Freesurfer] Help with QDEC Sig Cluster annotations and mri_convert and mri_annotation2label

I don't know about the gii question, but the labels can be created with mri_annotation2label specifying fsaverage as the subject doug On 07/31/2014 09:41 AM, Tara Ann Miskovich wrote: Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of

Re: [Freesurfer] Freesurfer Help

Hi Paras, The tcsh warning is ok, but see this link for more info and a fix: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg28980.html The unrecognized flag error is because you have a space between the dash and subjid, just delete that space. -Louis On Thu, 3 Jul 2014, Paras

[Freesurfer] Freesurfer Help

Dear Sir/Madam, I am a masters student at Newcastle University using Freesurfer to extract data from MRI scans. When trying to use the command lines in terminal, I seem to be getting an error message which I was wondering if you could help me with. The command line I am using is :

[Freesurfer] Help -Quality control of the splitting of midline structures?

Dear Freesurfers, I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to check how midline structures were split. I am concerned about how well my ACC ROIs line up with the midline of the brain, and

Re: [Freesurfer] Help -Quality control of the splitting of midline structures?

Hi Sarah do you want to look at the surfaces? This can actually be done in freeview if you don't mind messing around with the command line a bit (you can specify offsets and rotations for the surfaces so that you can see the medial wall if you want). Perhaps Ruopeng can comment? cheers

Re: [Freesurfer] Help with subject's functional overlay

Hi Doug, Me and Shahin have looked at the registration and it looks fine. I know the activation is 0 because when I click on those vertices it tells me the tksconcat.nii value is **0.00**. I looked at the cortex.label file and found the 0-valued vertices within the file. We have scanned the

Re: [Freesurfer] Help with subject's functional overlay

Is the cortex label 0 in the same locations where you have 0s in the surface mask? On 05/06/2014 12:07 PM, Cesar Echavarria wrote: Hi Doug, Me and Shahin have looked at the registration and it looks fine. I know the activation is 0 because when I click on those vertices it tells me the

Re: [Freesurfer] Help with subject's functional overlay

To add to my previous e-mail, it seems the surface masks differ from run to run. The run whose registration we revised manually seems to have no problem. We then use the registration from this run as the initial point for the registration of subsequent runs. These later runs do show those holes on

Re: [Freesurfer] Help with subject's functional overlay

but are there holes in the cortex label irrespective of what is happening in the fMRI? On 5/6/14 4:44 PM, Cesar Echavarria wrote: I looked at the surface mask and it seems those 0-valued vertices are 0-valued in the mask as well (image attached). Is there a way to correct this? To reiterate

Re: [Freesurfer] Help with subject's functional overlay

Hi Cesar what command lines did you run to register and sample? Bruce On Mon, 5 May 2014, Cesar Echavarria wrote: Hello freesurfer experts, The functional overlay for one of our subjects looks like the image attached. You'll notice the holes on the overlay that have a value of 0. I'm

Re: [Freesurfer] Help with subject's functional overlay

Hi Bruce, After unpacking the data, I simply run the selxavg command below and allow it to do the automatic pre-processing. selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh The analysis was generated with the following command: mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface

Re: [Freesurfer] Help with subject's functional overlay

It could be that the brain mask is too aggressive. Try looking at Subjects/myla/bold/RRR/masks/brain.nii.gz doug On 05/05/2014 03:17 PM, Cesar Echavarria wrote: Hi Bruce, After unpacking the data, I simply run the selxavg command below and allow it to do the automatic pre-processing.

Re: [Freesurfer] Help with subject's functional overlay

I used the command below to check the brain mask relative to the subject's anatomy: tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz The mask looked fine in that no portion of the brain appeared to lie outside the mask. Cesar On Mon, May 5, 2014 at 3:43 PM, Douglas N

Re: [Freesurfer] Help with subject's functional overlay

Have you checked the registration? If so, are you sure that the activation is exactly 0? Also, look at cortex.label to check whether somehow those vertices were not labeled. On 05/05/2014 04:08 PM, Cesar Echavarria wrote: I used the command below to check the brain mask relative to the

[Freesurfer] Help with Temporal horn

Hello, How can I generate volume for temporal horn, temporal white matter and temporal gray matter. Thanks Rashmi Sent from my iPhone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Help with Temporal horn

You can create an annotation of the lobels using mri_annoation2label with the --lobesStrict option. Once you have that you can run mri_aparc2aseg using the --wmparc option (look in the recon-all.log file for an example of how the wmparc.mgz is created), then use mri_segstats to get the

[Freesurfer] Help Thickness Reproducibility

Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~ mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su rf/lh.white -out_name /home/nf04/subjects/groupstudy/lh_std_60.mgh

Re: [Freesurfer] Help Thickness Reproducibility

The dimension mismatch means that the input data does not match the surface. It looks like the surface is from an individual but the input data is from a group analysis (which means fsaverage subject) On 01/23/2014 02:35 PM, Thiago Junqueira wrote: Dear FreeSurfers I am having some troubles

Re: [Freesurfer] help with save_nifti

Hi Doug, Thanks for your reply. I have the problem even if I use MRIread and MRIwrite. But I have done a little more digging following your suggestions. Basically, there are differences in the output of mri_vol2surf (that I should have spotted earlier), as well as differences in the header

Re: [Freesurfer] help with save_nifti

No idea why. What is the difference in the headers? Can you post the terminal output of both your mri_vol2surf commands? Also, you can try using MRIread.m and MRIwrite.m (these use load_nifti and save_nifti under the hood but also do some things to the header). doug On 11/20/2013 08:46 AM,

[Freesurfer] help with save_nifti

Hi, I am trying to save a nifti file using save_nifti. I'm running into a strange problem that I describe below. I have a nifti file (subj_mask.nii) created by a colleague using Nibabel (http://nipy.sourceforge.net/nibabel/). This volume is in the MNI305 space. Step1: In a first step I

[Freesurfer] Help with mri_copy_values

I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As I understand it, if I run mri_copy_values brainmask.mgz 0 wm.mgz all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be applied to the wm.mgz (provided they have the same geometry or some

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