[Freesurfer] Problems with mri_watershed and creating the BEM geometry file
Dear all, I have successfully run the freesurfer-steps for my subject and completed it without errors. After that I started MNE to create my BEM meshes. The manual tells me, for MNE to do that, the mri_watershed routine from freesurfer is used. Also, this runs fine, as far as the four surfaces (brain, inner_skull, outer_skull and outer_skin) are produced. Here is the problem: when MNE wants to create the BEM geometry file, it checks whether the surfaces are overlapping or not. Apparently they do: outer skin CM is 0.20 -3.31 10.19 mm Going from 5th to 4th subdivision of an icosahedron (ntri: 20480 -> 5120) outer skin CM is 0.20 -3.31 10.19 mm outer skull CM is 0.20 -3.19 9.75 mm inner skull CM is 0.08 -5.38 17.14 mm Checking that outer skull surface is inside outer skin surface...[ok] Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = -3.98566e-16 * 4*PI). Coulnd't create the geometry file Though I do not know what CM or these numbers in mm given mean, I can tell by using freeview, that the surfaces indeed overlap. My questions are now: which of all the files freesurfer created in the recon-all processes does the mri_watershed routine use? In other words, which of the surfs or transform do I have to check and manually edit to get rid of this problem? And which recon-processes do I have to run again? Is there an easier way around this problem? As always, help is very much appreciated. Thanks. Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tabel with labels and name of brain regions for both atlases
Dear all, I am trying to use my freesurfer data for fibertracking. So far it is working and I can even specifically tell the programm, which labels/brain regions to use. However, I haven't found an overview tabel, where all labels stand together with the region's name. It would be painfull, to open for every subject tksurfer and then moving with the mouse over the region of interest to get the correct label. Is there such a table overview for both atlases and where can I find them? Thank you. Sincerely, Maria Felber -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Talairach transformation
Hi Bruce, thanks for the first response. I tried to find some information on the webpage about xform, but failed. So what is xform standing for and where/how can I check it? As in the later processing stages I want to do localization and DCM-Modeling with my data, I guess the correct talairach coords are kind of important for later comparisons. Thanks again, Maria - Original Message - From: "Bruce Fischl" To: "Maria Felber" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 9, 2011 2:13:05 PM Subject: Re: [Freesurfer] Talairach transformation Hi Maria as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords. cheers Bruce p.s. not sure why it would be smaller On Fri, 9 Sep 2011, Maria Felber wrote: > Dear all, > > sorry, if that question came up before in the mailing list and I simple have > been unable to find the thread. > > Following the wiki reconstruction workflow, I ran yesterday the recon-all > -all process. The process finished without errors. So the next step was to > check the talairach transform. > Now, according to the FsTutorial/Talairach I have to make some adjustments > and then run the whole process again. That is all nice and good. > > However, why is it, that the talairach volume is always, no matter which > subject I look at, is always significantly smaller than the target volume? Is > that normal? Has it to be fixed? Or is that just normal? Attached find one > example. > As I am using freesurfer for the first time, I am really unsure about that. > > Thanks for the help, > Maria > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Talairach transformation
Hi Bruce,
so we are back at the beginning. After I ran recon-all -all, I did exactly that
and checked the xform using tkregister2. And here I always see that my
talairach volume (the transform) is always smaller, which can be very well seen
as the orig surfaces of the subjects are always a little outside the brain and
reach well into the skull areas. Of course I can make the adjustments as
descriped in the short instructions. But this also means I ran the recon-all
precess anew for another 30 h per subject.
And that is the reason, why I asked if this is normal that the tailarach
transform is a) always smaller than the original brain, and b) if I can make
any adjustments to prevent that from happening and thus saving another 30h per
subject.
In short: How acurate hat the talairach.xfm has to be and is it possible to
change some parameters to make this transformation a little more accurate while
running the recon-all process only once?
Best,
Maria
- Original Message -
From: "Bruce Fischl"
To: "Maria Felber"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, September 13, 2011 4:07:55 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Maria
you can use tkregister2 to check the accuracy of the talairach.xfm
transform ("xform" for short), and correct it if you want.
cheers
Bruce
On Tue, 13 Sep 2011, Maria Felber wrote:
> Hi Bruce,
>
> thanks for the first response. I tried to find some information on the
> webpage about xform, but failed. So what is xform standing for and where/how
> can I check it?
> As in the later processing stages I want to do localization and
DCM-Modeling with my data, I guess the correct talairach coords are kind of
important for later comparisons.
> Thanks again,
> Maria
>
> - Original Message -
> From: "Bruce Fischl"
> To: "Maria Felber"
> Cc: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, September 9, 2011 2:13:05 PM
> Subject: Re: [Freesurfer] Talairach transformation
>
> Hi Maria
>
> as long as the tal xform is reasonable I wouldn't worry about it, unless
> for some reason you care a lot about the accuracy of the talairach coords.
>
> cheers
> Bruce
>
> p.s. not sure why it would be smaller
>
> On Fri, 9 Sep 2011, Maria Felber wrote:
>
>> Dear all,
>>
>> sorry, if that question came up before in the mailing list and I simple have
>> been unable to find the thread.
>>
>> Following the wiki reconstruction workflow, I ran yesterday the recon-all
>> -all process. The process finished without errors. So the next step was to
>> check the talairach transform.
>> Now, according to the FsTutorial/Talairach I have to make some adjustments
>> and then run the whole process again. That is all nice and good.
>>
>> However, why is it, that the talairach volume is always, no matter which
>> subject I look at, is always significantly smaller than the target volume?
>> Is that normal? Has it to be fixed? Or is that just normal? Attached find
>> one example.
>> As I am using freesurfer for the first time, I am really unsure about that.
>>
>> Thanks for the help,
>> Maria
>>
>>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
--
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A
04103 Leipzig, Germany
Phone: +49 341 9940-2465/2522
--
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A
04103 Leipzig, Germany
Phone: +49 341 9940-2465/2522
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about
it or do you have something in progress which would fix this problem anytime
soon?
Thanks,
Maria
- Original Message -
From: "Avi Snyder"
To: "Sita Kakunoori" , fel...@cbs.mpg.de, "Avi
Snyder"
Cc: "Bruce Fischl"
Sent: Tuesday, September 13, 2011 11:03:28 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are
expected if the contrast properties of the sample image are far from those
of the target. This condition can easily occur if the target is based on
1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images
tend to be relatively bright in the center of the head.) Gd++ contrasted
MP-RAGE scans routinely do not produce decent atlas transforms unless
special measures are taken. A FreeSurfer fix for this problem is
theoretically feasible.
Avi
---
On 9/13/11 2:26 PM, "Sita Kakunoori" wrote:
>
>I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this
>e-mail.
>Hi Dr.Snyder, Not sure if you remember but we saw something similar in a
>dataset here at the center where the talairach was much smaller than the
>orig.mgz volume and you created a new talairach template to be used with
>that dataset. I just wondered if this issue is similar to that.
>
>Thanks much,
>Sita.
>-- Forwarded message --
>Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST)
>From: Maria Felber
>To: freesurfer@nmr.mgh.harvard.edu
>Subject: [Freesurfer] Talairach transformation
>
>Hi Bruce,
>
>so we are back at the beginning. After I ran recon-all -all, I did
>exactly that and checked the xform using tkregister2. And here I always
>see that my talairach volume (the transform) is always smaller, which can
>be very well seen as the orig surfaces of the subjects are always a
>little outside the brain and reach well into the skull areas. Of course I
>can make the adjustments as descriped in the short instructions. But this
>also means I ran the recon-all precess anew for another 30 h per subject.
>And that is the reason, why I asked if this is normal that the tailarach
>transform is a) always smaller than the original brain, and b) if I can
>make any adjustments to prevent that from happening and thus saving
>another 30h per subject.
>In short: How acurate hat the talairach.xfm has to be and is it possible
>to change some parameters to make this transformation a little more
>accurate while running the recon-all process only once?
>Best,
>Maria
>
>
>- Original Message -
>From: "Bruce Fischl"
>To: "Maria Felber"
>Cc: freesurfer@nmr.mgh.harvard.edu
>Sent: Tuesday, September 13, 2011 4:07:55 PM
>Subject: Re: [Freesurfer] Talairach transformation
>
>Hi Maria
>
>you can use tkregister2 to check the accuracy of the talairach.xfm
>transform ("xform" for short), and correct it if you want.
>
>cheers
>Bruce
>On Tue, 13 Sep 2011, Maria Felber wrote:
>
>> Hi Bruce,
>>
>> thanks for the first response. I tried to find some information on the
>>webpage about xform, but failed. So what is xform standing for and
>>where/how can I check it?
>> As in the later processing stages I want to do localization and
>DCM-Modeling with my data, I guess the correct talairach coords are kind
>of
>important for later comparisons.
>> Thanks again,
>> Maria
>>
>> - Original Message -
>> From: "Bruce Fischl"
>> To: "Maria Felber"
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Sent: Friday, September 9, 2011 2:13:05 PM
>> Subject: Re: [Freesurfer] Talairach transformation
>>
>> Hi Maria
>>
>> as long as the tal xform is reasonable I wouldn't worry about it, unless
>> for some reason you care a lot about the accuracy of the talairach
>>coords.
>>
>> cheers
>> Bruce
>>
>> p.s. not sure why it would be smaller
>>
>> On Fri, 9 Sep 2011, Maria Felber wrote:
>>
>>> Dear all,
>>>
>>> sorry, if that question came up before in the mailing list and I
>>>simple have been unable to find the thread.
>>>
>>> Following the wiki reconstruction workflow, I ran yesterday the
>>>recon-all -all process. The process finished without errors. So the
>>>next step was to check the talairach transform.
>>> Now, according to the FsTutorial/Talairach I have to make some
>>>adjustments and then run the whole process again. That is all nice and
>>>good.
>>>
>>> However, w
[Freesurfer] Fwd: Talairach transformation
Dear Ms. Kakunoori,
sorry to bother you again, but as I did not get a reply to my last message to
everyone so far troubled with my question, I am trying here for a second time.
It is indeed the case, that all my data were scanned with a 3T. And if that is
indeed the problem Dr. Snyder figured out, then what can I do about it? Or is
anyone already working on this problem? I can hardly imagine I am the only one
recording with a 3T instead of a 1.5T.
Yours sincerely,
Maria Felber
- Forwarded Message -
From: "Maria Felber"
To: "Avi Snyder"
Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\" , freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, September 15, 2011 10:46:55 AM
Subject: Re: [Freesurfer] Talairach transformation
Dear all,
indeed all my T1-scans were recorded with a 3T scanner. So what can I do about
it or do you have something in progress which would fix this problem anytime
soon?
Thanks,
Maria
- Original Message -
From: "Avi Snyder"
To: "Sita Kakunoori" , fel...@cbs.mpg.de, "Avi
Snyder"
Cc: "Bruce Fischl"
Sent: Tuesday, September 13, 2011 11:03:28 PM
Subject: Re: [Freesurfer] Talairach transformation
Hi Sita,
Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are
expected if the contrast properties of the sample image are far from those
of the target. This condition can easily occur if the target is based on
1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images
tend to be relatively bright in the center of the head.) Gd++ contrasted
MP-RAGE scans routinely do not produce decent atlas transforms unless
special measures are taken. A FreeSurfer fix for this problem is
theoretically feasible.
Avi
---
On 9/13/11 2:26 PM, "Sita Kakunoori" wrote:
>
>I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this
>e-mail.
>Hi Dr.Snyder, Not sure if you remember but we saw something similar in a
>dataset here at the center where the talairach was much smaller than the
>orig.mgz volume and you created a new talairach template to be used with
>that dataset. I just wondered if this issue is similar to that.
>
>Thanks much,
>Sita.
>-- Forwarded message --
>Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST)
>From: Maria Felber
>To: freesurfer@nmr.mgh.harvard.edu
>Subject: [Freesurfer] Talairach transformation
>
>Hi Bruce,
>
>so we are back at the beginning. After I ran recon-all -all, I did
>exactly that and checked the xform using tkregister2. And here I always
>see that my talairach volume (the transform) is always smaller, which can
>be very well seen as the orig surfaces of the subjects are always a
>little outside the brain and reach well into the skull areas. Of course I
>can make the adjustments as descriped in the short instructions. But this
>also means I ran the recon-all precess anew for another 30 h per subject.
>And that is the reason, why I asked if this is normal that the tailarach
>transform is a) always smaller than the original brain, and b) if I can
>make any adjustments to prevent that from happening and thus saving
>another 30h per subject.
>In short: How acurate hat the talairach.xfm has to be and is it possible
>to change some parameters to make this transformation a little more
>accurate while running the recon-all process only once?
>Best,
>Maria
>
>
>- Original Message -
>From: "Bruce Fischl"
>To: "Maria Felber"
>Cc: freesurfer@nmr.mgh.harvard.edu
>Sent: Tuesday, September 13, 2011 4:07:55 PM
>Subject: Re: [Freesurfer] Talairach transformation
>
>Hi Maria
>
>you can use tkregister2 to check the accuracy of the talairach.xfm
>transform ("xform" for short), and correct it if you want.
>
>cheers
>Bruce
>On Tue, 13 Sep 2011, Maria Felber wrote:
>
>> Hi Bruce,
>>
>> thanks for the first response. I tried to find some information on the
>>webpage about xform, but failed. So what is xform standing for and
>>where/how can I check it?
>> As in the later processing stages I want to do localization and
>DCM-Modeling with my data, I guess the correct talairach coords are kind
>of
>important for later comparisons.
>> Thanks again,
>> Maria
>>
>> - Original Message -
>> From: "Bruce Fischl"
>> To: "Maria Felber"
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Sent: Friday, September 9, 2011 2:13:05 PM
>> Subject: Re: [Freesurfer] Talairach transformation
>>
>> Hi Maria
>>
>> as long as the tal xform is reasonable I wouldn't worry about it, unless
>> for some reason you care a lot about the accuracy of the talairach
>&g
Re: [Freesurfer] Talairach transformation
Dear Nick, how do I best implement your suggestions in my command line? e.g. recon-all -all -use-mritotal -nuintensitycor-3T -s im30 or recon-all -motioncor -s im30 recon-all -talairach -use-mritotal -s im30 recon-all -all -nuintensitycor-3T -s im30 As I have not a clue what changes will be saved by freesurfer or wethere they are just overwritten by a new command, please advise have best to follow you advise. Thank you. Sincerely, Maria - Original Message - From: "Nick Schmansky" To: "Bruce Fischl" Cc: "Maria Felber" , s...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, September 28, 2011 10:53:08 PM Subject: Re: [Freesurfer] Fwd: Talairach transformation you could also try: -talairach -use-mritotal which will use an alternate talarairch alignment scheme (from the MNI). it sometimes works better (not necessary for 3T). you should also probably add: -nuintensitycor-3T to the end of your recon-all command, which will run the nu_correct stage optimized for 3T. it wont help you with your talairach issue, but will produce better results for 3T data downstream. n. On Wed, 2011-09-28 at 16:38 -0400, Bruce Fischl wrote: > Hi Maria > > have you tried running without the talairach stuff? Try -notalairach and > see if it works for you > > cheers > Bruce > On Wed, 28 Sep 2011, Maria Felber wrote: > > > Dear Ms. Kakunoori, > > > > sorry to bother you again, but as I did not get a reply to my last message > > to everyone so far troubled with my question, I am trying here for a second > > time. > > It is indeed the case, that all my data were scanned with a 3T. And if that > > is indeed the problem Dr. Snyder figured out, then what can I do about it? > > Or is anyone already working on this problem? I can hardly imagine I am the > > only one recording with a 3T instead of a 1.5T. > > Yours sincerely, > > Maria Felber > > > > - Forwarded Message - > > From: "Maria Felber" > > To: "Avi Snyder" > > Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\" > > , > > freesurfer@nmr.mgh.harvard.edu > > Sent: Thursday, September 15, 2011 10:46:55 AM > > Subject: Re: [Freesurfer] Talairach transformation > > > > Dear all, > > > > indeed all my T1-scans were recorded with a 3T scanner. So what can I do > > about it or do you have something in progress which would fix this problem > > anytime soon? > > Thanks, > > Maria > > > > - Original Message - > > From: "Avi Snyder" > > To: "Sita Kakunoori" , fel...@cbs.mpg.de, "Avi > > Snyder" > > Cc: "Bruce Fischl" > > Sent: Tuesday, September 13, 2011 11:03:28 PM > > Subject: Re: [Freesurfer] Talairach transformation > > > > Hi Sita, > > > > Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are > > expected if the contrast properties of the sample image are far from those > > of the target. This condition can easily occur if the target is based on > > 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images > > tend to be relatively bright in the center of the head.) Gd++ contrasted > > MP-RAGE scans routinely do not produce decent atlas transforms unless > > special measures are taken. A FreeSurfer fix for this problem is > > theoretically feasible. > > > > Avi > > --- > > On 9/13/11 2:26 PM, "Sita Kakunoori" wrote: > >> > >> I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this > >> e-mail. > >> Hi Dr.Snyder, Not sure if you remember but we saw something similar in a > >> dataset here at the center where the talairach was much smaller than the > >> orig.mgz volume and you created a new talairach template to be used with > >> that dataset. I just wondered if this issue is similar to that. > >> > >> Thanks much, > >> Sita. > >> -- Forwarded message -- > >> Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST) > >> From: Maria Felber > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: [Freesurfer] Talairach transformation > >> > >> Hi Bruce, > >> > >> so we are back at the beginning. After I ran recon-all -all, I did > >> exactly that and checked the xform using tkregister2. And here I always > >> see that my talairach volume (the transform) is always smaller, which can > >> be very well seen as the orig surfaces of the subjects are always a > >
[Freesurfer] saving adjustments under different names
Dear all, I have run the recon-all process on my subject im01. Now I am checking for errors and found some. I also found the solution steps. However, as far as I understand it, every time I make a change, this will be permanently done. Is there a way to keep the steps I have done so far and to same further changes to a new subject file, e.g. im01_skullcorrected. I would just like to backup the steps I have done in case I worsen the solution so far and in case I want to compare them. Also, is there a way that the results from recon-all are saved under a different name? Thanks, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to make lh.curv lh.sulc visible
Dear all, in the process of understanding freesurfer I like to see/inspect the created transforms visually. However, so far I am not able to see all the data that is stored in the transforms folder. So is it possible to see files like /transforms/lh.curv or /transfroms/lh.sulc? And if yes, what is the programm and command order? So far, I only figured out how to see data like /transforms/lh.pial lh.orig lh.inflated and so on. Thanks a lot, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to make lh.curv lh.sulc visible
Dear Bruce, thanks again for your quick help. And sorry for mixing up the directories. Best, Maria - Original Message - From: "Bruce Fischl" To: "Maria Felber" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 2, 2011 4:25:10 PM Subject: Re: [Freesurfer] how to make lh.curv lh.sulc visible Hi Maria, those files don't live in the transforms dir, they live in the surf dir. Further, pial, inflated and orig are surfaces with geometry and topology information, but sulc and curv are just scalar fields over the surface. You can display them on any of the surfaces using file->load curvature in tksurfer cheers Bruce On Fri, 2 Dec 2011, Maria Felber wrote: > Dear all, > > in the process of understanding freesurfer I like to see/inspect the created > transforms visually. However, so far I am not able to see all the data that > is stored in the transforms folder. > So is it possible to see files like /transforms/lh.curv or > /transfroms/lh.sulc? And if yes, what is the programm and command order? > So far, I only figured out how to see data like /transforms/lh.pial lh.orig > lh.inflated and so on. > Thanks a lot, > Maria > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
