[Freesurfer] Talairach failed error

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute the FreeSurfer outputs for one of my subjects. I get the following error when I run the recon-all command: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.00

Re: [Freesurfer] Talairach Failed: Distorted T1

:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 Sorry, what is the brainstem.dat file? Is that something we create? On 4/6/2021 7:53 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Douglas, Thanks again. Is this value in the brainstem.dat

Re: [Freesurfer] Talairach Failed: Distorted T1

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Wednesday, April 14, 2021 9:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1 Sorry, what is the brainstem.dat file? Is that something we

Re: [Freesurfer] Talairach Failed: Distorted T1

...@nmr.mgh.harvard.edu on behalf of Harkey, Thomas Jarrott *Sent:* Tuesday, March 30, 2021 6:03 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 External Email - Use Caution Douglas, Thank you for your help. Another question. The FreeSurfer wiki

Re: [Freesurfer] Talairach Failed: Distorted T1

regards, Thomas Harkey UAMS College of Medicine M3 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, March 25, 2021 9:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1

Re: [Freesurfer] Talairach Failed: Distorted T1

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, March 25, 2021 9:48 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial scan that only covers 25mm of the brain inferior-superior

Re: [Freesurfer] Talairach Failed: Distorted T1

Harkey UAMS College of Medicine M3 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, March 25, 2021 9:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1 That is an axial

Re: [Freesurfer] Talairach Failed: Distorted T1

...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursday, March 25, 2021 9:11 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject

Re: [Freesurfer] Talairach Failed: Distorted T1

2022 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Thursday, March 25, 2021 9:11 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failed: Distorted T1 It looks like something is wrong with your input. For

Re: [Freesurfer] Talairach Failed: Distorted T1

It looks like something is wrong with your input. For starters, the voxel size looks huge. Run mri_info subject/mri/orig/001.mgz and send the result On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote: External Email - Use Caution Hello, My name is Thomas Harkey and I am conducting r

Re: [Freesurfer] Talairach to RAS conversion

You can use this transform to go from talairach to mni305 http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html You can then reverse case #2 here https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems to go from MNI305 to individual RAS On 2/26/2021 10:24 AM, Nasiriavanaki, Zahra wrote: Hi

Re: [Freesurfer] Talairach to RAS conversion

Dear Doug, I wanted to follow up on this question. I appreciate if you could comment on it. Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Boston, MA, USA, 02129 On Feb 26, 2021, at 10:

Re: [Freesurfer] Talairach to RAS conversion

Hi Doug Thanks for your reply. They are talairach coordinates as it is mentioned in that paper. How may I convert the talairach to RAS? Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Bos

Re: [Freesurfer] Talairach to RAS conversion

Is the point truly talairach or is it mni152 or mni305. If 152 or 305, then this page will tell you how to do the conversion https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 2/24/2021 3:26 PM, Nasiriavanaki, Zahra wrote: Hi Freesurferers I have some talairach coordinates on the

[Freesurfer] Talairach to RAS conversion

Hi Freesurferers I have some talairach coordinates on the cortical surface (extracted from a paper) and I need to see their location on my fmri maps. I used "tksurfer> go to saved point “ to see the location of that coordinate on my map. However, that coordinate is in talairach. Should I conver

Re: [Freesurfer] Talairach Failure in recon-subject {Disarmed}

That is just the failure detection. Sometimes it generates a false positive. Did you check the transform? If the rest of the downstream processes (eg, aseg and surfaces) are ok, then you don't need to worrry On 12/21/2020 6:53 PM, Wei Shao wrote: External Email - Use Caution Hi, Freesu

[Freesurfer] Talairach Failure in recon-subject {Disarmed}

External Email - Use Caution Hi, Freesurfer team I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation

[Freesurfer] Talairach failed

External Email - Use Caution Hello Freesurfer Developers, I am new to Freesurfer and I am currently only using it to reconstruct the surface structure from MRI data in order to make 3D prints. That means that I only need the files lh.pial and rh.pial in the end. This works fin

Re: [Freesurfer] Talairach Transform failure

External Email - Use Caution The image quality is quite good. GM and WM contrast is excellent. There are no scanning artifacts. The only remarkable finding is that this individual has moderate brain atrophy, enlarged ventricles, and large white matter signal abnormalities (hypointe

Re: [Freesurfer] Talairach Transform failure

The first thing to do is to check your input data to make sure that something is not really wrong. Eg, a large artifact or unusual anatomy. On 1/17/19 5:35 AM, Daniel Ferreira wrote: > > External Email - Use Caution > > Thanks Greve. Yes, I mean that the moveable is completely black. How

Re: [Freesurfer] Talairach Transform failure

External Email - Use Caution Thanks Greve. Yes, I mean that the moveable is completely black. How should I continue from here? If the registration is so far off that it is out of the field of view, what should I do next? Thanks Dani El mié., 16 ene. 2019 a las 22:54, Greve, Doug

Re: [Freesurfer] Talairach Transform failure

when you say it does not load, do you mean that the moveable is blank/black? The terminal output indicates that it is being loaded. It is probably the case that the registration is so far off that it is out of the field of view On 1/16/19 11:30 AM, Daniel Ferreira wrote: > > External Em

Re: [Freesurfer] Talairach Transform failure

External Email - Use Caution Hi Greve, Thanks for your quick reply. I mean that tkregister2 loads the target volume (I think the original T1 it is) but it does not load the moveable volume as stated in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview: "You

Re: [Freesurfer] Talairach Transform failure

What do you mean that the tal volume does not load as a mov volume? Can you send the terminal output from tkregister2? On 1/16/19 10:01 AM, Daniel Ferreira wrote: External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking throug

[Freesurfer] Talairach Transform failure

External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down? T

[Freesurfer] Talairach Transform failure

External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri*

Re: [Freesurfer] Talairach failed in monkey brain

The file passed to --reg should be a registration file. This is a text file with the transformation matrix and a few other things, not a volume file. On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote: External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey br

[Freesurfer] Talairach failed in monkey brain

External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey brain, i encountered an error during talairach registration step, i have used tkregister2 to manually edit the registration but i have gotten error there too: tkregister2 --targ /usr/local/fr

Re: [Freesurfer] Talairach of ROI and FindClustersAndGotoMax

One of them will be mni305 coordinates, the other an approximation of talairach coordinates. I'd have to dig into the code to see which one was which. On 11/20/17 10:17 AM, Dongsheng Wu wrote: Dear Freesurfer Developers, I have two questions about coordinate of ROI when running the QDEC mod

Re: [Freesurfer] [Talairach failed when striping skull]

...@nmr.mgh.harvard.edu] On Behalf Of Yi Li Sent: Thursday, November 16, 2017 12:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] [Talairach failed when striping skull] Dear Douglas, This fails just on this one. Image seems good. I attached it in the previous mail but being held. Thanks

[Freesurfer] Talairach of ROI and FindClustersAndGotoMax

Dear Freesurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxsWghtVtx Annot 1 -

[Freesurfer] Talairach of ROI

Hello FreeSurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWPCWPLow CWPHi NVtxsWghtVtx Annot 1

Re: [Freesurfer] [Talairach failed when striping skull]

: Thursday, November 16, 2017 11:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [Talairach failed when striping skull] does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it? On 11/16/2017 11:32

Re: [Freesurfer] [Talairach failed when striping skull]

does this fail on all your subjects or just this one? Have you looked at the input image to make sure that there is nothing wrong with it? On 11/16/2017 11:32 AM, Yi Li wrote: > Hi FS expert, > > When I run recon-all -autorecon1 -subjid , the Talaitach transform > failed. Please see the attache

[Freesurfer] [Talairach failed when striping skull]

Hi FS expert, When I run recon-all -autorecon1 -subjid , the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks! Best Regards, Yi -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.

Re: [Freesurfer] Talairach registration error

Ok - thank you! I will speak to the person who generated the files then. On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve wrote: > I don't know how you (or someone else) generated the nifti files in the > first place, so I can't help there. If you did not generate them, then > talk to the person

Re: [Freesurfer] Talairach registration error

I don't know how you (or someone else) generated the nifti files in the first place, so I can't help there. If you did not generate them, then talk to the person who did. I do not really recommend trying to do it by hand. You can get AP and SI correctly, but you'll never know whether they are L

Re: [Freesurfer] Talairach registration error

Ah, I see - how would I be able to do either of those? And would I have to check the geometry of each scan individually? Not sure how that works, but I have a substantially large dataset. Thank you for your response! On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve wrote: > That means that geom

Re: [Freesurfer] Talairach registration error

That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file wit

[Freesurfer] Talairach registration error

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not

Re: [Freesurfer] Talairach registration error

the nifti file does not have the needed information in it. where did you get it from? On 9/5/17 8:42 PM, Ariana Vajdi wrote: Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountere

[Freesurfer] Talairach registration error

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not

Re: [Freesurfer] Talairach error

o: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Talairach error > > It is failing the tal registration check. Does the registration look ok? > If so, then run with -no-talcheck. > > > On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote: >> Hello FreeSurfer exp

Re: [Freesurfer] Talairach error

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, August 10, 2017 1:18 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach error It is failing the tal registration check. Does the registration look ok? If so, then run

Re: [Freesurfer] Talairach error

It is failing the tal registration check. Does the registration look ok? If so, then run with -no-talcheck. On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote: > Hello FreeSurfer experts, > > I have been running into a consistent problem of Talairach alignment > error in my recon-all for some of m

[Freesurfer] Talairach transform QA on pre-defaced subjects

Dear FS developers and expert users, I am preprocessing with freesurfer 6.0 recon-all a set of pre defaced subjects and the results are generally good, but the Talairach transform QA measure are terribly bad and exactly the same on all defaced: #

Re: [Freesurfer] Talairach Registration Error : recon-all -s

Dear Experts, according to the log, Vasudev is using version 5.3-HCP. Therefore I expect that he is running FreeSurfer inside HCP pipeline scripts.  The problem is that the use of 6.0 version with HCP pipeline scripts is not currently recommended. see http://www.mail-archive.com/freesurfer@nmr.

Re: [Freesurfer] Talairach Registration Error : recon-all -s

This error is due to an incompatibility between the version of perl shipped with ubuntu16 and the MINC tools shipped with freesurfer. This issue has been fixed in freesurfer version 6.0, which I recommend you download and install. https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > I

Re: [Freesurfer] Talairach Registration Error : recon-all -s

It was actually mri_nu_correct.mni. this is our script that calls some MNIC programs. What version of MINC are you using? On 02/16/2017 01:01 PM, Dev vasu wrote: > Dear FreeSurfer Developers, > > I am incurring Talairach registration error when i was running recon-all -s > > Error : > > recon-al

[Freesurfer] Talairach Registration Error : recon-all -s

Dear FreeSurfer Developers, I am incurring Talairach registration error when i was running recon-all -s Error : recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017 Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP Platform: Ubuntu 16.04 recon-all log

[Freesurfer] Talairach error in monkey brain

Dear Freesurfer experts, I'm using freesurfer to process my monkey brain data. It reported errors during Talairach registration step. So I added no-tal-check tag to run recon-all autorecon1 and used tkregister2 to manually edit registration. However, I couldn't let them perfectly fitted, espec

Re: [Freesurfer] "Talairach Transform: transforms/talairach.xfm ***FAILED***"

Hi Bruce, Thanks so much. So, how would I check if it actually failed or not? How would I turn off the checking? How would I manually correct it? Would running without it be essentially the same as turning off the checking (procedurally)? Best, Fred > On Sep 14, 2016, at 15:59, Bruce Fisch

Re: [Freesurfer] "Talairach Transform: transforms/talairach.xfm ***FAILED***"

Hi Fred have you checked the transform to see if it actually failed? If not, you can just turn off the checking. If it did, you can manually correct it (or run without it) cheers Bruce On Wed, 14 Sep 2016, Uquillas, Federico D'Oleire wrote: > Dear fellow FreeSurfer users, > > I can't get a su

[Freesurfer] "Talairach Transform: transforms/talairach.xfm ***FAILED***"

Dear fellow FreeSurfer users, I can't get a subject to recon-all all the way through without crashing, regardless of the FS version used (deleted and started from scratch several times). It always fails with a Talairach transform fail error. Wondering if anybody else has experienced this issue

[Freesurfer] Talairach Conversion

Hello, I wanted to use the function: mri_label2label to convert my label file into talairach space. This is the output that I am getting. On the mri_label2label information page, it says to use 'talairach' as the target subject which is what I did, but it cannot find 'talairach'. Does anyone have

[Freesurfer] Talairach Help

Hi all, I am attempting to check the registration of some subjects, following the instructions on the wiki here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview I ran the following command from my

Re: [Freesurfer] Talairach registration not aligned to horizontal axis but TARGET and MOVEABLE are aligned

On 4/26/15 12:03 AM, Paul Dhami wrote: Greetings FS experts, I'm currently getting myself familiar with FS, and thus was going through the processing of a few subjects. I have one subject whose anatomical is not aligned with the horizontal/x axis, as seen right after reconstruction of the r

Re: [Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer

I think it is just that tksurfer reports coordinates from the orig surface whereas the cluster summary reports coordinates from the white surface. We some how never got around to fixing this in tksurfer. doug On 04/02/2015 10:18 AM, Alexandra Tanner wrote: > Hi Doug and Freesurfers, > > I ran m

[Freesurfer] Talairach coordinate discrepancy mri_surfcluster vs tksurfer

Hi Doug and Freesurfers, I ran mri_surfcluster to generate coordinates for cluster maxima from a functional surface analysis. The summary text file generated by mri_surfcluster lists a bunch of information about the clusters, including talairach coordinates for each cluster peak (see example below

[Freesurfer] Talairach transformation

Dear list, I am new to Freesurfer and I have a doubt about the Talairach transformation. As far I understand, the Talairach transformation is applied to compute the surface representations. However, this seems to be a “hidden“ step, i.e. no volume is saved as Talairach transformed. Is this corr

Re: [Freesurfer] Talairach transformation

Hi Roberta we compute but do not apply the talairach transform, so all the volumes, surfaces, ROIs are in subject space, not talairach. cheers Bruce On Mon, 13 Oct 2014, Roberta Santoro wrote: Dear list,   I am new to Freesurfer and I have a doubt about the Talairach transformation. As

Re: [Freesurfer] talairach coordinates

You can use mri_label2label specifying your subject as the source and fsaverage as the target and --regmethod volume. This will convert the coordinates to mni305 space. You can then use read_label.m to load the label into matlab On 09/19/2014 09:32 AM, ri wrote: > Hi all > I was wondering whet

[Freesurfer] talairach coordinates

Hi all I was wondering whether it’s possible to get the talairach coordinates associated with each label in the segmentation. I would like to use Freesurfer’s segmentation for analysis in Matlab.How to create a text file with the talairach coordinates of each label (or of a specific label, by

[Freesurfer] Talairach failure in 5.3 but not in 5.2

Hello all, I have 2 subjects that failed autorecon-all at the same Talairach step. Both subjects successfully completed autorecon-all in version 5.2. Here is the output from one of the subjects. Any suggestions? Corinna # #@# Talairach Fri Feb 28 12:39

Re: [Freesurfer] talairach transformation error and general recon-all error

I looked at the nifti files in freeview. The orientation in freeview is correct, but it appears all of the T1s that resulted in an error are washed out in freeview. I can vaguely see the outline of the head, but there's a gray box covering the image. When I click on regions of bone or brain in t

Re: [Freesurfer] talairach transformation error and general recon-all error

It could be that SPM is setting some scaling factor in the nifti header that FS is not reading properly. Which version of FS are you using? doug On 12/17/2013 02:38 PM, JARED NIELSEN wrote: > I looked at the nifti files in freeview. The orientation in freeview is > correct, but it appears all

Re: [Freesurfer] talairach transformation error and general recon-all error

Hi Bruce, Thanks for your response. It's a bit of a pain to access the dicoms, but it's possible. The bigger problem now is that I can't get freeview to work. I type in freeview into the command line and receive the following error: freeview.bin: error while loading shared libraries: libvtkverd

Re: [Freesurfer] talairach transformation error and general recon-all error

Hi Jared for the ones that run quickly and end, it's because you haven't told it to do anything. The first couple of lines of the recon-all.log file give the command line as: Thu Dec 5 14:00:18 MST 2013 /mnt/NAS3/freesurfer/freesurfer//bin/recon-all -i Time3_28908_s11038064-0005-1-01-0

[Freesurfer] talairach transforms

Trying autorecon1 with the example data set Bert,there is error in talairach transforms.What would be the problem? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

[Freesurfer] talairach transforms

after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12 Terminal window display was as shown bellow Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-ce

Re: [Freesurfer] Talairach Failure Detection

Thanks a lot!,Pablo Date: Fri, 30 Aug 2013 11:38:26 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection Hi Pablo yes, any single file that is in the correct series should be fine Bruce On Fri

Re: [Freesurfer] Talairach Failure Detection

on...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Than

Re: [Freesurfer] Talairach Failure Detection

place of "nii.gz" file? Can > I use any of the MR.1.3.12.2 (listed above)? > Many thanks, > Pablo > ---- > From: pablon...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Date: Tue, 27 Aug 2013 17:14:04 + &g

Re: [Freesurfer] Talairach Failure Detection

I use any of the MR.1.3.12.2 (listed above)? Many thanks,PabloFrom: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philip

Re: [Freesurfer] Talairach Failure Detection

From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philips

Re: [Freesurfer] Talairach Failure Detection

analyze format. Thank you for your support,Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 + Subject: Re: [Freesurfer] Talairach Failure Detection Hi I have one last question. I just noticed that my images are in Philips format. Would

Re: [Freesurfer] Talairach Failure Detection

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote: > Thank you very much for your input. Yes, I did start with analyze format and > also I have visually inspected the images. Almost all my > scans consiste

Re: [Freesurfer] Talairach Failure Detection

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection Hi Pablo have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines

Re: [Freesurfer] Talairach Failure Detection

best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct? Best,Pablo Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fis...@nmr.mgh.harvard.edu To: pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection Hi Pablo

Re: [Freesurfer] Talairach Failure Detection

Hi Pablo have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly cheers Bruce On Tue, 27

[Freesurfer] Talairach Failure Detection

Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attent

[Freesurfer] Talairach Failure Detection

Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects. I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attention,P

Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly.

y Windows Phone From: Bruce Fischl<mailto:fis...@nmr.mgh.harvard.edu> Sent: ‎8/‎18/‎2013 10:08 PM To: West, John D.<mailto:jdw...@iupui.edu> Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Talairach error - Talair

Re: [Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hi John can you send the entire recon-all.log? Any indication why the talairach.xfm was not created? cheers Bruce On Sun, 18 Aug 2013, West, John D. wrote: > Hello. > > We are trying to run freesurfer on a Super Computing system here at IU. > Unfortunately, we keep running into the following

[Freesurfer] Talairach error - Talairach file seems to not be written correctly.

Hello. We are trying to run freesurfer on a Super Computing system here at IU. Unfortunately, we keep running into the following error: # #@# Talairach Failure Detection Sun Aug 18 14:17:32 EDT 2013 /N/dc/projects/shenlab/subjects/10025_5/mri talai

Re: [Freesurfer] Talairach vs. MNI coordinates in FreeSurfer

Hi Juergen, yes use --nofixmni if you wan MNI coordinates. Note that there is no such thing as "MNI Talairach" coordinates. It is either MNI or Talairach, but not both! best doug On 8/14/13 8:50 AM, Jürgen Hänggi wrote: > Dear FS experts > > When extracting cluster information using mri_surfc

[Freesurfer] Talairach vs. MNI coordinates in FreeSurfer

Dear FS experts When extracting cluster information using mri_surfcluster, there is a problem with the --fixmni option. By default, FixMNI is 1 but it reports Talairach coordinates as confirmed by tksurfer. When using the option --nofixmni (FixMNI is zero) it reports MNI Talairach coordinates. Th

Re: [Freesurfer] talairach and MNI305 Atlas

Mark, you can run recon-all -s subject -motioncor -talairach And it will run it upto the creation of the talairach matrix. If you only have one run, then you don't need -motioncor doug On 07/15/2013 12:35 PM, Mark Plantz wrote: > Hello freesurfers, > > I am currently attempting to crea

Re: [Freesurfer] talairach and MNI305 Atlas

Hi Mark do you have a segmentaton for the brain? Bruce On Mon, 15 Jul 2013, Mark Plantz wrote: Hello freesurfers,     I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for inf

[Freesurfer] talairach and MNI305 Atlas

Hello freesurfers, I am currently attempting to create a normalized .mgz file from an input brain using mri_ca_normalize. Ultimately, I will use the norm.mgz file to create a .gca atlas for infant MRI's. Currently, I have three of the four required arguments. I am lacking the talairach.lta

Re: [Freesurfer] Talairach manual correction

Hi Andreia, you don't need a separate flag. It will automatically see that you have manually edited the talairach.xfm and not overwrite it. doug On 03/22/2013 11:48 AM, _andre...@sapo.pt wrote: > Hello! > > After completing the talairach correction in tkregister2 (saving the > changes with the

[Freesurfer] Talairach manual correction

Hello! After completing the talairach correction in tkregister2 (saving the changes with the SAVEREG button), I am running recon-all -all -s subj. But now I'm wondering if by doing it this way the changes will be incorporated or the process will start from the beggining leaving everything

[Freesurfer] Talairach General Question

Hi, I have a rather general, and perhaps even naive, concern regarding the Talairach transform. I've noticed that the coronal and/or horizontal views of the Talairach transform viewed under tkregister2, though generally correctly aligned with respect to the midline of the brain, they tend to have

Re: [Freesurfer] talairach transformation troubleshooting problem

I have total of 46 subjects with pre and post scans44 subjects were OK >>> using the stable version. >>> >>> Catherine >>> >>> >>> From: Bruce Fischl >>> To: Rongxiang Tang >>> Cc: Nick Schmansky ; Zeke Kaufman >

Re: [Freesurfer] talairach transformation troubleshooting problem

10:32 AM, Rongxiang Tang wrote: > >> I have total of 46 subjects with pre and post scans44 subjects were OK >> using the stable version. >> >> Catherine >> >> >> From: Bruce Fischl >> To: Rongxiang Tang >> Cc: Nick Sch

Re: [Freesurfer] talairach transformation troubleshooting problem

urfer@nmr.mgh.harvard.edu" Sent: Thursday, February 14, 2013 2:42 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem probably not, although it's hard to say. If you upload the whole subject dir I'll take a look. How does the aseg look? On Thu, 14 Feb 2013,

Re: [Freesurfer] talairach transformation troubleshooting problem

trol points to solve the > problem. > > Thanks, > Catherine > > *From:* Bruce Fischl > *To:* Rongxiang Tang > *Sent:* Thursday, February 14, 2013 2:03 PM > *Subject:* Re: [Freesurfer] talaira

Re: [Freesurfer] talairach transformation troubleshooting problem

Fischl To: Rongxiang Tang Sent: Thursday, February 14, 2013 2:03 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Al

Re: [Freesurfer] talairach transformation troubleshooting problem

Hi Catherine can you send us an image of what you are looking at? thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing th

[Freesurfer] talairach transformation troubleshooting problem

Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matte

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