Re: [Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?

Dear Kiyotaka, It is okay to distribute the buckner_data we post on our website for tutorial purposes. Allison On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wrote: > Dear FreeSurfer experts, > > We are planning to have a one-day neuroimaging workshop in Japan. One topic

[Freesurfer] FreeSurfer Boston Course Registration now open!

the waiting list every time we held a course so don't be dismayed if you end up on the waiting list. Allison Stevens  Lab Manager/Course Organizer FreeSurfer Development Team  Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical

[Freesurfer] FreeSurfer Course Registration now open!

and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. Allison Stevens > Lab Manager > FreeSurfer Development Team > Laboratory for Comp

[Freesurfer] Deadline to sign up for Copenhagen Course is near!

Hi everyone, There is just a week and a half left before the deadline to sign up for the FreeSurfer course being held in Copenhagen, Denmark on August 10th through the 12th. The deadline is June 1st. We still have a few places left! You can sign up for one here:

[Freesurfer] August FreeSurfer course in Copenhagen, Denmark

for this course, please visit: http://fscph2016.nru.dk/ Please feel free to contact my friends at NRU (cc'd) with any questions. Allison Stevens Lab Manager/Course Organizer Laboratory for Computational Neuroimaging FreeSurfer Development Team ___ Freesurfer

[Freesurfer] Postdoc position at Martinos Center for Biomedical Imaging

Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts General Hospital / Harvard Medical School The Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging has a job opening for a post-doctoral fellow to work on modeling cortical layers and

[Freesurfer] FreeSurfer Course to be held in Sao Paulo, Brazil

Hi everyone, There will be a FreeSurfer course held in Sao Paulo, Brazil on March 9th. It will be taught by 4 of our FreeSurfer team members. Please see the Sao Paulo section of our website for links to more information, who to contact with questions, and how to register:

Re: [Freesurfer] Fwd: Underinclusion of Gray Matter

You could also add a lot more voxels to the wm.mgz (beyond what is wm) and depending on the source of the problem, that could fix it. On Mon, 3 Nov 2014, Bruce Fischl wrote: Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white

[Freesurfer] 8 spots remain in the FreeSurfer course

Hello everyone, We have 8 spots remaining in our upcoming FreeSurfer course happening on October 27-29. We will accept late registrations up to the course date; however, since the payment deadline has passed, payment is due immediately upon registration. Details on the course and a link to the

Re: [Freesurfer] Boston FreeSurfer Course

On Mon, 29 Sep 2014, Allison Stevens wrote: Hello everyone, The next FreeSurfer Course will be held October 27th-29th at the Martinos Center in Charlestown, Massachusetts. Registration for the course is now open: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription **Important: If we do

[Freesurfer] Boston FreeSurfer Course

arrangements until you have received an *email confirmation* that you successfully registered for the course. Allison Stevens Lab Manager FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149

Re: [Freesurfer] 2 available spots in Boston FreeSurfer course

: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Friday, April 18, 2014 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 2 available spots in Boston FreeSurfer course We have had some last minute drop outs

[Freesurfer] 2 available spots in Boston FreeSurfer course

We have had some last minute drop outs and there are now 2 spots available in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to sign up for these spots, please register here: https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi Note that credit card cannot

[Freesurfer] FreeSurfer Course in Copenhagen

FreeSurfer Course Copenhagen 2014 We are pleased to announce a European FreeSurfer Course that will be held from August 11th to 13th 2014 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital and the Department for Computer

[Freesurfer] The FreeSurfer lab is seeking Research Technicians

Please see the job descriptions at the following links: https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchTechnologist Allison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] hippocampus region in an atlas?

The entire hippocampus is currently labeled by default in the recon-all stream. You can see it in the aseg.mgz (in the mri directory) and find volume information in stats/aseg.stats. To get the hippocampal subfields you have to run recon-all with an additional flag. This is documented here:

Re: [Freesurfer] how to obtain subjects cortical thickness and then analyze unpair t-test

Hi Rujing, If you are looking for the cortical thickness measures of a subject, you can find it in that subject's freesurfer directory in the 'stats' folder. In there, you will find a file called ?h.aparc.stats - one for each hemisphere. Within the stats file, you'll see the Average thickness

Re: [Freesurfer] recon all question

Hi Rashmi, You can find an explanation of the various measures we offer here: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Allison On Fri, 13 Sep 2013, Rashmi Singh wrote: I am doing volumetric studies where instead of using ICV, I use total brain volume as a co-variate. This

Re: [Freesurfer] Longitudinal processing

In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: As I'm having trouble importing nifti files

Re: [Freesurfer] Longitudinal processing

process exits with errors. On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote: In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running

Re: [Freesurfer] question about autorecon2-cp, autorecon-pial and autorecon-wm flags

That's correct. On Thu, 14 Mar 2013, Mehul Sampat wrote: Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the

Re: [Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample

Hi Kev, For the two scenarios you mentioned, here are my best estimates. I assume a healthy, adult population scanned with our recommended sequences. Any other type of dataset (pediatric, one with some type of pathology, one acquired long ago using a less than optimal sequence or coil, etc.)

Re: [Freesurfer] cannot allocate memory issue

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:02 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It looks like there is too huge a topology error

Re: [Freesurfer] cannot allocate memory issue

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, May 14, 2012 1:37 PM To: Allison Stevens Player Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It says that it couldn't open rh.orig.nofix and lh.orig.nofix

Re: [Freesurfer] cannot allocate memory issue

rh.orig.nofix and lh.orig.nofix. On the popup image, it doesn't look like the skull is present, but it does look like the cerebellum is. From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:28 PM To: Borzello, Mia Cc

Re: [Freesurfer] cannot allocate memory issue

that my last resort since it takes a day to complete. Thanks, m From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:16 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot

Re: [Freesurfer] longitudinal analysis 5.0 or 5.1?

Hi Cat, You'll need to rerun those subjects with 5.1 to be able to use the longitudinal analysis in 5.1. You can also find a detailed explanation on how to go about edits here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits Allison On Wed, 18 Apr 2012, Cat Chong wrote:   Dear

Re: [Freesurfer] Segmentation

Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change

Re: [Freesurfer] freeview

You can make a copy of the LUT and remove all regions from it you don't want to see. Then when you load you volume, specify you want to use this new LUT and you will only see the ROIs in it. Allison On Apr 12, 2012, at 11:40 PM, Adil Javed aj...@yahoo.com wrote: Hi, is there any way to

Re: [Freesurfer] created a new subcortical atlas; what's next?

Anthony, Depending on what version of FreeSurfer you are running, you would have to run the command it would normally run to create the aseg but substitute in your atlas. For example, in v5.1: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 You can see the step next to

Re: [Freesurfer] correcting pial surface

Julia, could you send a snapshot of the area in question? On Apr 2, 2012, at 5:33 AM, Richter, Julia julia.rich...@med.uni-heidelberg.de wrote: Dear freesurfer experts, I have several subjects whose cortical grey matter isn't included in the pial surface. Is there any possibility to

Re: [Freesurfer] Running FS on deskulled dataset

Hi Darshan, There are instructions on how to do this here: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F Allison On Tue, 27 Mar 2012, Darshan P wrote: I have an MRI volume dataset, which is deskulled beforehand . 

[Freesurfer] Spot Opened in Boston FreeSurfer course

Hi everyone, We had a last minute drop-out from our Boston FreeSurfer course which takes place April 2nd through the 4th. If anyone is interested in taking this spot, please let me know. Details about the course content, the registration fee, and other logistics can be found here:

[Freesurfer] FreeSurfer Course in Amsterdam!

Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website:

Re: [Freesurfer] Question regarding control points

Although the white surface finds its place based on intensity, it's starting point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you mention, drawing in some voxels combined with the intensity changes that come from the control points may help. Allison On Mar 12, 2012, at

Re: [Freesurfer] Recommended reconstruction wiki

Hi Martijn, autorecon-cp is correct, we start the process a bit earlier now. But even better, regardless of what edits you make, you can rerun with recon-all -make all and it will start at the earliest needed step. (Although running from autorecon2 after the skullstrip fix is correct as well).

Re: [Freesurfer] Recommended reconstruction wiki

with ERRORS at Fri Mar 2 14:23:15 CET 2012 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Best, Martijn On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens Player astev...@nmr.mgh.harvard.edu wrote: Hi Martijn, autorecon

Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.

the orig volume to the MNI305 atlas, so the spatial normalization in FreeSurfer is still done in volume space but not in surface space, right? Best, Xiangyu On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player astev...@nmr.mgh.harvard.edu wrote: Maybe you can apply the transform

Re: [Freesurfer] Fixing talairach registration

I don't think there is any other way. Is the talairach really that bad in all of your data? It won't recon without fixing it? On Feb 22, 2012, at 6:17 PM, cloud.c...@me.com wrote: After reading the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand that

Re: [Freesurfer] white matter edits

Vincent, Some may look like holes but as you mention are just sulci being cut through by that plane. A way to check if it is the above is to put the cursor on the surface that creates this hole and then toggle to the other views (sagittal, axial, coronal). It will become clearer whether it is

Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.

Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for? http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable On Feb 22, 2012, at 11:26 AM, Long longspac...@gmail.com wrote: Dear all, I had EPI images and T1 image

Re: [Freesurfer] Incorrect pial surface

Okay, I'll take a look. Allison On Mon, 17 Oct 2011, Jordan Pierce wrote: We've uploaded the file as 30193retry.tar.gz   Jordan Pierce ___ ___ Freesurfer mailing list

Re: [Freesurfer] undo pial edits only

Hi Torsten, If you run: recon-all -all -clean-bm -s subjid This should trask all the edits you made to the brainmask volume and make a new one to replace that. It will keep all your other edits. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: to correct the pial surface for incorrect

Re: [Freesurfer] tkmedit window size

Hi Torsten, I believe we have this on our to do list for tkmedit fixes. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: Hi there, I was wondering whether there is better option to resize the tkmedit window: when I drag it bigger, it appears that the same change in aspect ratio is applied

Re: [Freesurfer] (no subject)

Hi Heather, The cerebellum is not included in 5.1's total subcortical gm or total gm volumes. Let me double check on what is included in the subcortical gray matter total volume. Allison On Mon, 3 Oct 2011, Lugar, Heather wrote: Can you please tell me if the cerebellum is included in

Re: [Freesurfer] orig surface button

Hi Antonella, When you load the files that those buttons are associated with, then they become active. When you loaded the orig surfaces, the orig surface button still was not active? If you choose any button besides the Navigate button, when you left click, that will move the cursor (red

Re: [Freesurfer] Multiecho sequences available for Siemens

Hi Brian, Meet Andre who I believe can help you. Allison On Wed, 20 Jul 2011, Brian C. Schweinsburg, Ph.D. wrote: Hi Folks, I noticed in the multiecho portion of the freesurfer wiki that it says custom multiecho sequences are available from Martinos for use. I was wondering who I might

Re: [Freesurfer] Aseg and Cerebellum

If it is, you can try running the skullstrip step a second time. On Jul 20, 2011, at 7:14 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael, if cerebellar gray matter is not something you are terribly interested in quantifying then you are fine. cheers Bruce On Wed, 20

Re: [Freesurfer] Freesurfer and VBM

Fatima, I can't really say anything on this topic but I did want to point you to some information on FreeSurfer vs. VBM: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.WhataretheadvantagesofFreeSurferoverVBM.3F Allison On Fri, 8 Jul 2011, Ahmed, F, Me fah...@sun.ac.za wrote:

Re: [Freesurfer] Error using tkmedit

Hi Antonella, I found similar problems in the FreeSurfer mailing list archives: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07366.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03433.html

Re: [Freesurfer] WM edits with tkmedit make no difference

Hi Joel, Can you send Khoa (cc'd) the case and we'll look at what might be going on and then give you pointers on editing strategy? Directions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Allison On Fri, 3 Jun 2011, Joel Bruss wrote: I have a subject run through

Re: [Freesurfer] FreeSurfer Tutorial and Workshop

Registration is not open yet and that date is tentative. Once the date is confirmed and registration open, an email will be sent out to the Course mailing list which has a link on the top of the Course Description wiki. Allison On Fri, 27 May 2011, Eisenstein, Sarah wrote: Does anyone know

Re: [Freesurfer] What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?

Which version of FreeSurfer are you using? In the more recent versions, they are the same. Cortical White Matter is all the white matter contained within the white surface minus the subcortical gray matter and ventricles, etc. On May 20, 2011, at 7:37 AM, Righart, Ruthger Dr.

Re: [Freesurfer] stop receiving emails

You can unsubscribe here: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer On Thu, 12 May 2011, Krista Kelly wrote: How do I stop receiving emails from everyone asking and responding to questions about FreeSurfer? ___ Freesurfer mailing

Re: [Freesurfer] inflated surface

When you look at the case in tkmedit, in that same area, do you see an error? Looking at your snapshot, it looks like it could be normal. On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear FreeSurfer list, When I look at inflated surface of my subjects (healthy

Re: [Freesurfer] about recon-all

yep that's a typo. sorry! On Apr 25, 2011, at 9:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, I think that's a typo and should be autorecon2. Perhaps Nick can confirm? On Mon, 25 Apr 2011, Xiaoying Tang wrote: Hi All,I find the following content on the wikipage of

Re: [Freesurfer] hyperintense artifact causing problems for segmentation

Hi Sarah, Nick will be out of the office until next week. I would suggest just trying to run the default gcut and if you find you need to tweak it a bit, doing mri_gcut --help will describe the parameter (-T) that you can adjust for a cleaner skullstrip. You could also run -skullstrip a second

Re: [Freesurfer] Frontal lobes excluded

Hi Sean, Yes, we can help. Best would be to upload the subject and Khoa can take a look. She can give you additional instructions if needed. Allison On Mon, 18 Apr 2011, Seán Froudist Walsh wrote: Dear FreeSurfer gurus, I have T1 scans of a patient at three different time-points (one run

Re: [Freesurfer] install tracula

John, Tracula is available in the soon to be released 5.1 but not in 5.1. Allison On Fri, 15 Apr 2011, John Fredy wrote: Hello all I am doing the tutorial about tracula ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but I can`t find the trac-all command in my system. I was

Re: [Freesurfer] install tracula

Sorry, I meant not in 5.0. On Fri, Apr 15, 2011 at 19:29, Allison Stevens astev...@nmr.mgh.harvard.edu wrote: John, Tracula is available in the soon to be released 5.1 but not in 5.1. Allison On Fri, 15 Apr 2011, John Fredy wrote: Hello all I am doing the tutorial about tracula ( http

Re: [Freesurfer] recon-all on version 4.5

Hi Saad, Since there is no message indicating it stopped due to error, I would try running it again as it most likely stopped due to the machine it was running on. You can pick up where it left off by doing: recon-all -make all -s mysubject On Apr 7, 2011, at 12:25 AM, Saad Ramadan

Re: [Freesurfer] gcut

Hi Michael, With 5.0, gcut is run by default I believe. If you look at the recon-all.log for that subject and search for gcut, you should be able to see if it ran. Allison On Thu, 7 Apr 2011, Dougherty, Michael wrote: Hello all, I would like to take advantage of the gcut feature to remove

Re: [Freesurfer] wmparc

Hi Jose, I believe we just got rid of redundant information. The subcortical structures are in the aseg.stats and don't need to be in the wmparc.stats. On Wed, 6 Apr 2011, Jose Soares wrote: Hi all, I am working with FS 4.5 and 5.0 and I have noticed that in wmparc.stats in 5.0 there are

Re: [Freesurfer] Pial surface correction failure after adding control points

in. Pls see the attachment. Does anyone encounter the same thing before? Thank you for advice! Min On Thu, Mar 31, 2011 at 1:11 PM, Allison Stevens astev...@nmr.mgh.harvard.edu wrote: Hi Min, We've learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2

Re: [Freesurfer] Pial surface correction failure after adding control points

Hi Min, We've learned that -autorecon2-cp might not be doing what was intended. Try runing -autorecon2 and see if it fixes everything. Allison On Thu, 31 Mar 2011, Min Liu wrote: Dear Freesurfer users, My first run of recon12 left some white and grey matter at temporal pole region excluded.

Re: [Freesurfer] Bad orientation/registration in the motion correction step

You can run the old command and then start the processing from that step on I think. On Mar 30, 2011, at 4:23 AM, Nikolas Borrel-Jensen nikolasbor...@gmail.com wrote: Hello! I have found a solution for the problem causing the bad registration. In Freesurfer 5.0, the function

Re: [Freesurfer] How to proceed after manual edit of segmentation

You can just rerun autorecon2 and autorecon3. If you save it as aseg.mgz, it will recognize edits were made when you rerun. On Mar 30, 2011, at 7:51 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear FreeSurfer list, I am making some manual correction to subcortical structures using Edit

Re: [Freesurfer] tkmedit undo volume?

Hi Allison, Can you send me the link to the wiki page that says that? To my knowledge, you can only undo the very last edit you made in tkmedit and that is by going to Edit undo. With freeview, you can select undo as many times as you'd like. Allison On Wed, 16 Mar 2011, Nugent, Allison C.

Re: [Freesurfer] Re-post: Fixated brain

Tibor, We are working to put some exvivo wm segmentation methods into the next FreeSurfer release although I'm not sure where that stands. We do process our exvivo scans with FreeSurfer but we use scripts that use different parameters than recon-all since the contrast is different and as you

Re: [Freesurfer] results visualization

Hi Nadia, You can follow instructions on how to check data using our tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData and https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData Allison On Tue, 15 Mar 2011, nadia merhoum wrote: Hello I have just

Re: [Freesurfer] Pial surface error

Allie, It's hard to tell from that one slice but the pial surface grows out from the wm surface so most likely, in order to fix that error, you will have to find where the white surface is inaccurate and add or remove voxels on the wm.mgz. Allison On Fri, 11 Mar 2011, Allie Rosen wrote: Hi,

Re: [Freesurfer] about recon-all command

That flag is needed if your input is larger than the required size by FreeSurfer 256x256x256. You would not use it on input that did not require it (ie it is smaller than 256x256x256). On Mar 10, 2011, at 4:53 AM, Kenichiro Tanaka ktan...@j-adni.org wrote: Hello All, I have a question

Re: [Freesurfer] tutorial course

Sorry, Pom - the course is full. You can sign up for the course mailing list to hear about upcoming courses: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi Allison On Fri, 25 Feb 2011, Pom Sailasuta wrote: Hello, Is it too late to register for the April tutorial course at

Re: [Freesurfer] subcortical roi

Hi Fabrizio, You can use mri_extract_label for this. You need to specify the index number of the structure which you can find here: $FREESURFER_HOME/FreeSurferColorLUT.txt On Tue, 15 Feb 2011, fabrizio piras wrote: Dear FS experts, I run recon all on several patients, manual edited all the

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

as' as directed in the recommended recon workflow. Thanks, Cheryl On 1/31/11 7:05 PM, Allison Stevens astev...@nmr.mgh.harvard.edu wrote: Hi Cheryl, 1) Yes, just use save not save as 2) this information is already generated and can be found in the aseg.stats in each subject's stats dir. Some

Re: [Freesurfer] Manual editing of skull strip and mri_segstats

Hi Cheryl, 1) Yes, just use save not save as 2) this information is already generated and can be found in the aseg.stats in each subject's stats dir. Some of the information is at the top of that file. On Mon, 31 Jan 2011, Cheryl McCreary wrote: Hi, I'm new to Freesurfer and am trying to

Re: [Freesurfer] Can I mix different versions of freesurfer

Rong, You should wait until 5.1 comes out and use that to rerun your cross-sectionals (which will have to be rerun to match a newer version) and use that longitudinal stream which will be the most reliable. Allison On Thu, 23 Dec 2010, rong chen wrote: Hi, I want to use FreeSurfer to analyze

Re: [Freesurfer] WM surface and Deep Brain nuclei

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison On Wed, 22 Dec 2010, Luke Bloy wrote: Hello, I'm new to freeSurfer and just starting to look

Re: [Freesurfer] WM surface and Deep Brain nuclei

PM, Allison Stevens wrote: Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison On Wed, 22 Dec 2010, Luke Bloy wrote: Hello, I'm

Re: [Freesurfer] report with mri_segstats

Could you let me know what version you are running and the full asegstats2table command? To put it in Excel, I open Excel first then go to File Open, select the .txt file created by using asegstats2table (I've never used the -delimiter flag) and from there a box pops up where you can choose

Re: [Freesurfer] WM parcelleted boundary

Would the wmparc.mgz work for this? It should be in the mri dir. -- On Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote: Hi, Is there a way to get the cortical parcellations projected onto the WM boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber tracking. Please

Re: [Freesurfer] Rerunning recon-all after editing aseg

What version are you using? -- On Thu, 9 Dec 2010, Jennifer Addicks wrote: Hello, I manually edited the aseg.mgz file for one of my participants, I was wondering if someone could tell me how to rerun the recon-all to ensure that these changes are incorporated in future steps and

Re: [Freesurfer] control points-- Any tips?

You want to make sure you are placing the control points only on wm voxels that are 110 and wm voxels that are at least 1 voxel away from a gm voxel in all directions. If you'd like, you could send me a snapshot of where you placed the control points and I can give you feedback on that. You

Re: [Freesurfer] severe recon-all errors only in v5.0

Andreas, Could you send us one of these subjects so we can take a look? Allison -- On Mon, 22 Nov 2010, Andreas Berger wrote: Hello Surfers, we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4

Re: [Freesurfer] recon1: brain missing

Suzanne, You could try running different watershed thresholds to see if it fixes the problem without having to clone it in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix Allison -- On Fri, 19 Nov 2010, suzanne oosterwijk wrote: Hi, I have been running recon1 recently

Re: [Freesurfer] BrainSegVol different in wmparc and aseg

Jeff, Yes, you would only want to take it from the aseg.stats. I believe this is fixed or on the list to be fixed for future versions. Allison -- On Fri, 12 Nov 2010, Jeff Sadino wrote: bump :) On Tue, Nov 9, 2010 at 11:38 AM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, When I

Re: [Freesurfer] Talairach failure detection error

Hi Kristina, You can find the answer to your question here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F As a new user, you might find that FAQ helpful. Allison -- On Wed, 3 Nov 2010, Rapuano, Kristina

Re: [Freesurfer] Make functional ROI's from clusters

Alice, You might find this tutorial helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual and mri_volcluster or mri_surfcluster Allison -- On Tue, 26 Oct 2010, Alice Albrecht wrote: Hi Everyone, I'm new to freesurfer so I apologize if my question has

Re: [Freesurfer] Total GM and WM volumes

Ed, I would use the values in the aseg.stats. I'm not sure why there is this difference (Doug might be able to elaborate on how the values in aseg.stats are calculated) but for v5.0, we went over how all the stats were being calculated and make sure the values in the aseg.stats were the most

Re: [Freesurfer] Total GM and WM volumes

are present. Is there no subcortical wm volume present or defined? Ed On 27 Oct 2010, at 15:58, Allison Stevens wrote: Ed, I would use the values in the aseg.stats. I'm not sure why there is this difference (Doug might be able to elaborate on how the values in aseg.stats

Re: [Freesurfer] ERROR: mpr2mni305 failed

What does it say in transforms/talairach_avi.log? -- On Thu, 14 Oct 2010, Maria Luisa Mandelli wrote: Hi! I get this error running recon_all Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see

Re: [Freesurfer] memory needed to run a freesurfer stream

Nathan, You can find that info here: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements -- On Thu, 7 Oct 2010, Nathan Dankner wrote: Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm

Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

None should be the first label in the FreeSurferColorLUT.txt (it's labeled as Unknown with an ID# of 0). But really you should be labeling it what it truly is. Is this the gray matter you are labeling as CSF? -- On Thu, 7 Oct 2010, Wang, Xin wrote: one more question: I replace the

Re: [Freesurfer] Marking four majors lobes: frontal, parietal, temporal, occipital

Mustafa, There are a couple of relevant pages with information on this. These: http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13908.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04901.html Allison -- On Wed,

Re: [Freesurfer] Pial Edit on Atrophied Brain

You can try to add voxels to the wm.mgz in the area that you know is wm. If that's already there or you tried that already, let us know. Allison -- On Wed, 6 Oct 2010, Soon Hock Wei wrote: Dear All: Just to follow up with my previous enquiry, is there any suggestion/advice over this pial

Re: [Freesurfer] Siemens Trio 3T imaging parameters

http://www.nmr.mgh.harvard.edu/~andre/ -- On Fri, 16 Jul 2010, Tricia Merkley wrote: Hi Freesurfers, Does anyone have a suggestion for an optimal scanner protocol for structural scans using Siemens Trio 3T? Thanks, Tricia Merkley ___

Re: [Freesurfer] recon-all -all finished without error but didn't produce aseg.mgz files

What does the recon-all.log file in the stats dir show for the steps it missed? Allison -- On Mon, 12 Jul 2010 aekai...@umich.edu wrote: Hi all, I just ran recon-all -s (subject) -all for several subjects and it looked like they ran successfully, however when I went to check the data in

Re: [Freesurfer] recon-all -all finished without error but didn't produce aseg.mgz files

voxels, peak = 94), gca=93.5 STOPPED RUNNING HERE *** if anyone can recognize this step so I don't have to run full recon again that would be great or any ideas as to why this happend best, Anson K. University of Michigan On Mon, 12 Jul 2010 11:39:10 -0400 (EDT), Allison Stevens

Re: [Freesurfer] Troubleshooting: Are these pial and wm surface acceptable?

The areas near subcortical structures are not included in thickness estimates. If you load your subject in tksurfer and load the aparc.annot you will see a section on the medial side called unknown. If the regions you are concerned about fall within here, then you do not have to worry about it

Re: [Freesurfer] Creating table of segmentation volumes

Please use the aseg.stats for the corpus callosum. wmparc.stats should be used only for the wm parcellations. This will be fixed in the next release of freesurfer. -- On Mon, 12 Jul 2010, liang wang wrote: Hi, I was starting to create a table of segmentation volumes corresponding to

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