Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

[Joseph Dien]

Oops, never mind.  User error.  I’m too embarrassed to even explain what I did. 
 :)

Joe

> On Feb 29, 2016, at 21:38, Joseph Dien  wrote:
> 
> Hi,
>   I’m having an fsgd error that has totally stumped me.  I’m trying to run 
> the following command to compute the second level statistics:
> 
> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
> normAcc.mtx
> 
> I get the error message:
> 
> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
> gdfReadHeader: reading RPA-accGT.fsgd
> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
> 
> I used the utility flip to make sure the file was in UNIX format (with 
> linefeeds).
> I then double-checked by reading in the binary codes with Matlab’s fread and 
> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
> 
> Here is the contents of the fsgd file.
> 
> GroupDescriptorFile 1
> Title RP1
> Class Main
> Variables LogoAcc NormAcc OrthAcc PhonAcc
> Input RPA903  Main0.750.790.770.62
> Input RPA906  Main0.810.810.830.74
> Input RPA907  Main0.871   0.840.83
> Input RPA908  Main0.910.930.950.89
> Input RPA909  Main0.740.950.720.72
> Input RPA910  Main0.850.960.810.79
> Input RPA912  Main0.750.780.730.73
> Input RPA914  Main0.7 0.850.830.81
> Input RPA915  Main0.850.890.750.83
> Input RPA916  Main0.840.920.870.72
> Input RPA917  Main0.830.930.920.83
> Input RPA918  Main0.870.910.790.85
> Input RPA919  Main0.860.960.910.88
> Input RPA920  Main0.840.920.870.84
> Input RPA921  Main0.870.920.880.85
> Input RPA922  Main0.8 0.9 0.9 0.72
> 
> What’s really driving me to distraction is that a previous version of this 
> file (with a different set of participants) works fine.  I’m attaching both.  
> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
> fread, the first 85 characters (first four lines) of both files are identical.
> 
> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
> 
> Any help would be greatly appreciated!
> 
> Joe
> 
> 
> 
> 
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com
> Cell Phone: 202-297-8117
> http://joedien.com
> 
> ___
> Freesurfer mailing list
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> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Those numbers only refer to the color the too will appear: hence the name color 
lookup table
hth
d

Sent from my Phone

> On Mar 1, 2016, at 21:33, Faeze Vedaei  wrote:
> 
> Thank you for your response. It is better to explain my question that the 
> coordinates for paracentral in .ctab file is '63 100 60', that you changed 
> these to '23 230 60' in your new version. My question is that how you applied 
> such this change on the RBG values for this region?
> 
> Regards,
> Faezeh
> 
>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei  wrote:
>> Thank you so much for you response. I should say that I know about what you 
>> are saying. My issue is that I have these 4 columns in my LUT file. Why and 
>> how can I change the numbers (RGB values) to create new LUT?
>> 
>> Bests,
>> Faezeh
>> 
>>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
>>> Hi,
>>> 
>>> Thank you so much for you descriptions. I checked out the link you just 
>>> sent me. Because I do not have many experiences working with Freesurfer, I 
>>> really could not understand about how I can do such this revising in LUT 
>>> file. Can you explain more about this? I truly appreciate your time and 
>>> help.
>>> 
>>> Regards,
>>> Faezeh Vedaei
>>> 
 On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
 Hi,
 
 I really appreciate you for help me in this process. May you clarify me 
 from which pattern you changed the RGB values for that region? How I can 
 change the coordinates for the others?
 
 Regards,
 Faezeh Vedaei
 
 
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  
> wrote:
> Hi,
> 
> I should let you know that, it works! It shows paracentral name in 
> tksurfer. So, how I have to revise my .ctab file to get the right result?
> 
> Regards,
> Faezeh Vedaei
> 
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  
>> wrote:
>> Hi,
>> 
>> Thank you for your response. I just used the command you suggested to 
>> use by just a change in calling .ctab LUT file. I used the path: 
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>> just calling aparc.annot.a2009s.ctab. It is strange that I created annot 
>> file for lh.G_and_S_paracentral.label, but it shows its name in 
>> tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what 
>> is your opinion?
>> 
>> Regards,
>> Faezeh Vedaei
>> 
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  
>>> wrote:
>>> Hi,
>>> 
>>> 
>>> Here is the text format of those files.
>>> 
>>> Regards,
>>> Faezeh Vedaei
>>> 
 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  
 wrote:
 Hi
 
 Thank you so much for your response. I attached here three files 
 including the command lines, LUT file , and the list of names I want 
 to get and what the result is actually. I'd appreciate if you look at 
 them and let me know what is wrong with that. 
 
 Regards,
 Faezeh Vedaei
 
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  
> wrote:
> Hi,
> 
> I checked again to arrange the labels in the order of LUT file, but 
> the result has not changed. Can you help me more how I can fix this 
> problem? Thank you so much for your time and help.
> 
> Regards,
> Faezeh Vedaei
> 
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>  wrote:
>> Hi,
>> 
>> Thank you for your response. Yes, you are right. The names come from 
>> the color LUT file. But, the issue is that I chose the label files 
>> from that LUT file too. It meas the source that I chose the label 
>> files from and the source of the region's names in tksurfer are the 
>> same. The problem is just I do not have the label's names I merged 
>> to create annot file, in the tksurfer GUI. It shows another names of 
>> that list! So, what do you think about? What is the problem?
>> 
>> Regards,
>> Faezeh Vedaei
>> 
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>>>  wrote:
>>> Hi Freesurfer experts,
>>> 
>>> I have created an annotation file by several label files using 
>>> mris_label2annot command in Freesurfer. The problem is that when I 
>>> open this annot file in tksurfer and click on colored regions which 
>>> corresponded to specific labels I had chosen them, I do not have 
>>> their name on the vertex information part at the bottom of 

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Thank you for your response. It is better to explain my question that the
coordinates for paracentral in .ctab file is '63 100 60', that you changed
these to '23 230 60' in your new version. My question is that how you
applied such this change on the RBG values for this region?

Regards,
Faezeh

On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei  wrote:

> Thank you so much for you response. I should say that I know about what
> you are saying. My issue is that I have these 4 columns in my LUT file. Why
> and how can I change the numbers (RGB values) to create new LUT?
>
> Bests,
> Faezeh
>
> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you so much for you descriptions. I checked out the link you just
>> sent me. Because I do not have many experiences working with Freesurfer, I
>> really could not understand about how I can do such this revising in LUT
>> file. Can you explain more about this? I truly appreciate your time and
>> help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> I really appreciate you for help me in this process. May you clarify me
>>> from which pattern you changed the RGB values for that region? How I can
>>> change the coordinates for the others?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>>
>>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 I should let you know that, it works! It shows paracentral name in
 tksurfer. So, how I have to revise my .ctab file to get the right result?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> Thank you for your response. I just used the command you suggested to
> use by just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to 
>>> get
>>> and what the result is actually. I'd appreciate if you look at them and 
>>> let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> > wrote:
>>>
 Hi,

 I checked again to arrange the labels in the order of LUT file, but
 the result has not changed. Can you help me more how I can fix this
 problem? Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei <
 faezeved...@gmail.com> wrote:

> Hi,
>
> Thank you for your response. Yes, you are right. The names come
> from the color LUT file. But, the issue is that I chose the label 
> files
> from that LUT file too. It meas the source that I chose the label 
> files
> from and the source of the region's names in tksurfer are the same. 
> The
> problem is just I do not have the label's names I merged to create 
> annot
> file, in the tksurfer GUI. It shows another names of that list! So, 
> what do
> you think about? What is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei <
> faezeved...@gmail.com> wrote:
>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I 
>> open
>> this annot file in tksurfer and click on colored regions which 
>> corresponded
>> to specific labels I had chosen them, I do not have their name on the
>> vertex information part at the bottom of tksurfer GUI. It shows very
>> different names for these regions. May you explains me what is the 
>> problem
>> I could not see the exact region's name as I have them for label 
>> files?
>>
>> Thanks,

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

It is just a text file (you can open it with vi or gedit whatever),
just add new lines for new labels and make the colors the color you
want them to be.\

hth
d

On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei  wrote:
> Thank you so much for you response. I should say that I know about what you
> are saying. My issue is that I have these 4 columns in my LUT file. Why and
> how can I change the numbers (RGB values) to create new LUT?
>
> Bests,
> Faezeh
>
> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you so much for you descriptions. I checked out the link you just
>> sent me. Because I do not have many experiences working with Freesurfer, I
>> really could not understand about how I can do such this revising in LUT
>> file. Can you explain more about this? I truly appreciate your time and
>> help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I really appreciate you for help me in this process. May you clarify me
>>> from which pattern you changed the RGB values for that region? How I can
>>> change the coordinates for the others?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>>
>>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I should let you know that, it works! It shows paracentral name in
 tksurfer. So, how I have to revise my .ctab file to get the right result?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> Thank you for your response. I just used the command you suggested to
> use by just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file 
> for
> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to 
>>> get
>>> and what the result is actually. I'd appreciate if you look at them and 
>>> let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I checked again to arrange the labels in the order of LUT file, but
 the result has not changed. Can you help me more how I can fix this 
 problem?
 Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei
  wrote:
>
> Hi,
>
> Thank you for your response. Yes, you are right. The names come
> from the color LUT file. But, the issue is that I chose the label 
> files from
> that LUT file too. It meas the source that I chose the label files 
> from and
> the source of the region's names in tksurfer are the same. The 
> problem is
> just I do not have the label's names I merged to create annot file, 
> in the
> tksurfer GUI. It shows another names of that list! So, what do you 
> think
> about? What is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
>  wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I 
>> open this
>> annot file in tksurfer and click on colored regions which 
>> corresponded to
>> specific labels I had chosen them, I do not have their name on the 
>> vertex
>> information part at the bottom of tksurfer GUI. It shows very 
>> different
>> names for these regions. May you explains me what is the problem I 
>> could not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>

>>>
>>
>

>>>
>>
>
>
> 

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Thank you so much for you response. I should say that I know about what you
are saying. My issue is that I have these 4 columns in my LUT file. Why and
how can I change the numbers (RGB values) to create new LUT?

Bests,
Faezeh

On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:

> Hi,
>
> Thank you so much for you descriptions. I checked out the link you just
> sent me. Because I do not have many experiences working with Freesurfer, I
> really could not understand about how I can do such this revising in LUT
> file. Can you explain more about this? I truly appreciate your time and
> help.
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I really appreciate you for help me in this process. May you clarify me
>> from which pattern you changed the RGB values for that region? How I can
>> change the coordinates for the others?
>>
>> Regards,
>> Faezeh Vedaei
>>
>>
>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> I should let you know that, it works! It shows paracentral name in
>>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 Thank you for your response. I just used the command you suggested to
 use by just a change in calling .ctab LUT file. I used the path:
 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
 calling aparc.annot.a2009s.ctab. It is strange that I created annot file
 for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
 G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
 opinion?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
 wrote:

> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
> wrote:
>
>> Hi
>>
>> Thank you so much for your response. I attached here three files
>> including the command lines, LUT file , and the list of names I want to 
>> get
>> and what the result is actually. I'd appreciate if you look at them and 
>> let
>> me know what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but
>>> the result has not changed. Can you help me more how I can fix this
>>> problem? Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> > wrote:
>>>
 Hi,

 Thank you for your response. Yes, you are right. The names come
 from the color LUT file. But, the issue is that I chose the label files
 from that LUT file too. It meas the source that I chose the label files
 from and the source of the region's names in tksurfer are the same. The
 problem is just I do not have the label's names I merged to create 
 annot
 file, in the tksurfer GUI. It shows another names of that list! So, 
 what do
 you think about? What is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei <
 faezeved...@gmail.com> wrote:

> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I 
> open
> this annot file in tksurfer and click on colored regions which 
> corresponded
> to specific labels I had chosen them, I do not have their name on the
> vertex information part at the bottom of tksurfer GUI. It shows very
> different names for these regions. May you explains me what is the 
> problem
> I could not see the exact region's name as I have them for label 
> files?
>
> Thanks,
> Faezeh Vedaei
>


>>>
>>
>

>>>
>>
>
___
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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 

Re: [Freesurfer] running two versions of fs in the same

[Bruce Fischl]

is it just the BA labels you want out of the newer version? If so, just 
change your FREESURFER_HOME to point at the new version after your 5.1 
recon-all is done and run the -dobalabels target with the dev recon-all


cheers
Bruce
On 
Tue, 1 Mar 2016, Fengji Geng wrote:




Hi Bruce,

 

The command that we ran is  recon-all.

 

Below is the error msg:

 

mri_label2label --srcsubject fsaverage --srclabel
/export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject
HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface

 

No such file or directory

mri_label2label: could not open label file
/export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label

 

srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label

srcsubject = fsaverage

trgsubject = HMN122

trglabel = ./lh.BA2.label

regmethod = surface

 

srchemi = lh

trghemi = lh

trgsurface = white

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

usehash = 1

Use ProjAbs  = 0, 0

Use ProjFrac = 0, 0

DoPaint 0

 

SUBJECTS_DIR    /export/data/hippocampus/HMN/data

FREESURFER_HOME /cell_root/software/freesurfer/current/sys

Loading source label.

Invalid argument

ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label

Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23
12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016

 

 

 

 

---
---

Hi Fengji

 

you need to give us more details about the problems before we can help

you. What commands failed? What was the screen output?

 

Note that there is still no such thing as FS 6.0. We are hoping to have it

in the relatively near term, but it doesn't exist yet.

 

cheers

Bruce

 

 

On Tue, 1 Mar 2016,

Fengji Geng wrote:

 

> Dear fs developers,?

>

> we are attempting to use the stable version of fs 5.1 for processing while

> also using the most current version for hippocampal segmentation on the
same

> set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when

> the develop version of fs 6 was installed, we began having an issue with
the

> fsaverage folder linking to the newest version, when we need it to link to

> version 5.1 during processing. The label files that we need for processing

> in version 5.1 are not accessible in the new version?s fsaverage

> folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016,
we

> never had this issue. So, we are wondering if the newest develop version
of

> fs 6.0 does not allow?two versions of fs to be used in the same data.?

>

> Looking forward to hearing from you and thanks in advance.

>

> Best,

>

> - Fengji

 

---

Fengji

 


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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

The 4 number columns represent:
Red Green Blue and Alpha

The numbers range from 0-255. They can be combined to create any
color. Play around, and you will see what it does.

hth,
d

On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you so much for you descriptions. I checked out the link you just sent
> me. Because I do not have many experiences working with Freesurfer, I really
> could not understand about how I can do such this revising in LUT file. Can
> you explain more about this? I truly appreciate your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I really appreciate you for help me in this process. May you clarify me
>> from which pattern you changed the RGB values for that region? How I can
>> change the coordinates for the others?
>>
>> Regards,
>> Faezeh Vedaei
>>
>>
>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I should let you know that, it works! It shows paracentral name in
>>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. I just used the command you suggested to
 use by just a change in calling .ctab LUT file. I used the path:
 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
 calling aparc.annot.a2009s.ctab. It is strange that I created annot file 
 for
 lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
 G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
 opinion?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
 wrote:
>
> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
> wrote:
>>
>> Hi
>>
>> Thank you so much for your response. I attached here three files
>> including the command lines, LUT file , and the list of names I want to 
>> get
>> and what the result is actually. I'd appreciate if you look at them and 
>> let
>> me know what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but
>>> the result has not changed. Can you help me more how I can fix this 
>>> problem?
>>> Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. Yes, you are right. The names come from
 the color LUT file. But, the issue is that I chose the label files 
 from that
 LUT file too. It meas the source that I chose the label files from and 
 the
 source of the region's names in tksurfer are the same. The problem is 
 just I
 do not have the label's names I merged to create annot file, in the 
 tksurfer
 GUI. It shows another names of that list! So, what do you think about? 
 What
 is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
  wrote:
>
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I 
> open this
> annot file in tksurfer and click on colored regions which 
> corresponded to
> specific labels I had chosen them, I do not have their name on the 
> vertex
> information part at the bottom of tksurfer GUI. It shows very 
> different
> names for these regions. May you explains me what is the problem I 
> could not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei


>>>
>>
>

>>>
>>
>
>
> ___
> 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 

Re: [Freesurfer] running two versions of fs in the same

[Fengji Geng]

Hi Bruce,

The command that we ran is  recon-all.

Below is the error msg:

mri_label2label --srcsubject fsaverage --srclabel 
/export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject 
HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface

No such file or directory
mri_label2label: could not open label file 
/export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label

srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label
srcsubject = fsaverage
trgsubject = HMN122
trglabel = ./lh.BA2.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/export/data/hippocampus/HMN/data
FREESURFER_HOME /cell_root/software/freesurfer/current/sys
Loading source label.
Invalid argument
ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label
Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 
EST 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016




--

Hi Fengji



you need to give us more details about the problems before we can help

you. What commands failed? What was the screen output?



Note that there is still no such thing as FS 6.0. We are hoping to have it

in the relatively near term, but it doesn't exist yet.



cheers

Bruce





On Tue, 1 Mar 2016,

Fengji Geng wrote:



> Dear fs developers,?

>

> we are attempting to use the stable version of fs 5.1 for processing while

> also using the most current version for hippocampal segmentation on the same

> set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when

> the develop version of fs 6 was installed, we began having an issue with the

> fsaverage folder linking to the newest version, when we need it to link to

> version 5.1 during processing. The label files that we need for processing

> in version 5.1 are not accessible in the new version?s fsaverage

> folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016, we

> never had this issue. So, we are wondering if the newest develop version of

> fs 6.0 does not allow?two versions of fs to be used in the same data.?

>

> Looking forward to hearing from you and thanks in advance.

>

> Best,

>

> - Fengji

---
Fengji

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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

Thank you so much for you descriptions. I checked out the link you just
sent me. Because I do not have many experiences working with Freesurfer, I
really could not understand about how I can do such this revising in LUT
file. Can you explain more about this? I truly appreciate your time and
help.

Regards,
Faezeh Vedaei

On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:

> Hi,
>
> I really appreciate you for help me in this process. May you clarify me
> from which pattern you changed the RGB values for that region? How I can
> change the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested to
>>> use by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
>>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
 wrote:

> Hi
>
> Thank you so much for your response. I attached here three files
> including the command lines, LUT file , and the list of names I want to 
> get
> and what the result is actually. I'd appreciate if you look at them and 
> let
> me know what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but
>> the result has not changed. Can you help me more how I can fix this
>> problem? Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from
>>> the color LUT file. But, the issue is that I chose the label files from
>>> that LUT file too. It meas the source that I chose the label files from 
>>> and
>>> the source of the region's names in tksurfer are the same. The problem 
>>> is
>>> just I do not have the label's names I merged to create annot file, in 
>>> the
>>> tksurfer GUI. It shows another names of that list! So, what do you think
>>> about? What is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei <
>>> faezeved...@gmail.com> wrote:
>>>
 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I open
 this annot file in tksurfer and click on colored regions which 
 corresponded
 to specific labels I had chosen them, I do not have their name on the
 vertex information part at the bottom of tksurfer GUI. It shows very
 different names for these regions. May you explains me what is the 
 problem
 I could not see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei

>>>
>>>
>>
>

>>>
>>
>
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Re: [Freesurfer] mri_label2vol projfrac missing voxels

[dgw]

Hi,

I just wanted to post back the problem was solved (Thanks Doug). The
solution is this:

1. use mri_aparc2aseg
mri_aparc2aseg --s $SUBJECT --o .mgz --annot 
--annot-table 


[Note, in my case I was using 3 different values, 1, 2, 3 for the
labels with only left hemisphere labels (the details will change for
people with different label numbers etc.)]
2. read in the resulting file (python or matlab: pick your poison).
set all voxels less than 1001 to 0, set all voxels greater than 1003
to 0, remap voxels with value 1001 to 1, 1002 to 2 1003 to 3.

Now you are done and can load with your clut file.

hth
d

On Mon, Feb 29, 2016 at 2:16 PM, dgw  wrote:
> Hi,
>
> I just wanted to repost this question. After turning on the
> transparency, I also noticed that this problem goes both directions
> (i.e. some voxels which aren't gray matter in the lh.ribbon.mgz are
> labeled utilized when calling mri_label2vol.
>
> On Tue, Feb 23, 2016 at 3:19 PM, dgw  wrote:
>> Hi,
>>
>> I am having trouble with the projfrac option in mri_label2vol (on the
>> current dev freesurfer environment). When I use the following command:
>>
>> mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o
>> lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1
>> .01
>>
>> I get many missed voxels from the gray matter (see the attached image,
>> with the yellow representing the label overlaid on the ribbon.mgz). I
>> have tried more extreme delta values and this doesn't help. (note
>> scrolling to nearby slices indicates the neighboring voxels are
>> included, so it isn't from the angle projecting oddly (that is why I
>> took a slice from the middle of this large label)). Is there a better
>> way to convert the annotation to a volume just in the gray matter, but
>> including all of the relevant voxels?
>>
>> Is there a fundamental algorithmic difference between mris_volmask and
>> mri_label2vol?
>>
>> If yes, why?
>>
>> Thanks,
>> D
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Re: [Freesurfer] running two versions of fs in the same dataset

[Bruce Fischl]

Hi Fengji

you need to give us more details about the problems before we can help 
you. What commands failed? What was the screen output?


Note that there is still no such thing as FS 6.0. We are hoping to have it 
in the relatively near term, but it doesn't exist yet.


cheers
Bruce


On Tue, 1 Mar 2016, 
Fengji Geng wrote:



Dear fs developers, 

we are attempting to use the stable version of fs 5.1 for processing while
also using the most current version for hippocampal segmentation on the same
set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when
the develop version of fs 6 was installed, we began having an issue with the
fsaverage folder linking to the newest version, when we need it to link to
version 5.1 during processing. The label files that we need for processing
in version 5.1 are not accessible in the new version’s fsaverage
folder. However, before we updated to fs 6.0 dev version on 28-Jan-2016, we
never had this issue. So, we are wondering if the newest develop version of
fs 6.0 does not allow two versions of fs to be used in the same data. 

Looking forward to hearing from you and thanks in advance.

Best,

- Fengji


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Re: [Freesurfer] Entorhinal Cortex segmentation and volume

[Bruce Fischl]

Hi Melina

Sorry for the delay in responindg, can you tell us a bit more about the 
acquisition? They look very grainy and low contrast.

Bruce


On Mon, 16 Feb 2015, Melina Lehnerer wrote:

> Thank you both for your respond.
> 1. I have attached you some pictures. Like douglas wrote it corresponds to 
> white matter in aseg, but is more often labelled as "none" than "cortex 
> unknown". So is this "normal" and can I trust those borders? Or would you 
> rather advise to control aseg and aparc segmentation to estimate the 
> entorhinal cortex segmentation?
>
> 2. You're right, Bruce, in freeview the exvivo label it just follows the 
> surface. So I'll try mri_label2vol.
>
> Cheers Melina
>
> Am 16.02.2015 um 16:33 schrieb Douglas Greve:
>> On 2/16/15 9:31 AM, Bruce Fischl wrote:
>>> Hi Melina
>>> 
>>> 1. Can you send us a picture? I'm not sure given your description,
>>> although the surfaces can be arbitrary in the hippocampus/amygdala and
>>> should be ignored there.
>> This corresponds to  the "cortex unknown" label in aparc (and is
>> probably labeled WM in the aseg). This is normal.
>>> 2. You should be able to use mri_label2vol for this. Note that you can 
>>> load
>>> the label itself directly into freeview if you want without needing to run
>>> label2vol (but it will follow the white surface I believe and not fill the
>>> ribbon)
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Mon, 16 Feb 2015, Melina Lehnerer wrote:
>>> 
 Hi experts,
 I'm rather unexperienced with freesurfer so please excuse my basic
 requests.
 1. I controlled the segmentation of the entorhinal cortex (EC) in over
 50 subjects following the borders described in Fischl 2009 (Predicting
 the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg
 aparc-aseg.mgz.
 I noticed (esp. in the coronar slices and in approximately every mri)
 brain tissue between amygdala/ hippocampus/ temporalpole and the EC
 labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the
 segmentation? Or is a label (e.g. perirhinal cortex) not loaded?
 
 2. Is there a possibility to visualize the EC volume in freeview or
 tkmedit from the exvivo.stats or exvivo.label file? I would like to
 compare it to the other EC volume because they have very different
 volumes. In the mail archive were similar questions about that but you
 haven't answered them yet.
 
 Many thanks in advance,
 Melina
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>> ___
>> 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.
>> 
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Check this page out for details. The values are just numbers in the
columns of the file:

https://en.wikipedia.org/wiki/RGB_color_model

hth
d

On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
> Hi,
>
> I really appreciate you for help me in this process. May you clarify me from
> which pattern you changed the RGB values for that region? How I can change
> the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested to use
>>> by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
>>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>>> wrote:

 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
 wrote:
>
> Hi
>
> Thank you so much for your response. I attached here three files
> including the command lines, LUT file , and the list of names I want to 
> get
> and what the result is actually. I'd appreciate if you look at them and 
> let
> me know what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but
>> the result has not changed. Can you help me more how I can fix this 
>> problem?
>> Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from
>>> the color LUT file. But, the issue is that I chose the label files from 
>>> that
>>> LUT file too. It meas the source that I chose the label files from and 
>>> the
>>> source of the region's names in tksurfer are the same. The problem is 
>>> just I
>>> do not have the label's names I merged to create annot file, in the 
>>> tksurfer
>>> GUI. It shows another names of that list! So, what do you think about? 
>>> What
>>> is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
>>>  wrote:

 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I 
 open this
 annot file in tksurfer and click on colored regions which corresponded 
 to
 specific labels I had chosen them, I do not have their name on the 
 vertex
 information part at the bottom of tksurfer GUI. It shows very different
 names for these regions. May you explains me what is the problem I 
 could not
 see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei
>>>
>>>
>>
>

>>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
> 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
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

I really appreciate you for help me in this process. May you clarify me
from which pattern you changed the RGB values for that region? How I can
change the coordinates for the others?

Regards,
Faezeh Vedaei


On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  wrote:

> Hi,
>
> I should let you know that, it works! It shows paracentral name in
> tksurfer. So, how I have to revise my .ctab file to get the right result?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you for your response. I just used the command you suggested to use
>> by just a change in calling .ctab LUT file. I used the path:
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>> opinion?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> Here is the text format of those files.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi

 Thank you so much for your response. I attached here three files
 including the command lines, LUT file , and the list of names I want to get
 and what the result is actually. I'd appreciate if you look at them and let
 me know what is wrong with that.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but
> the result has not changed. Can you help me more how I can fix this
> problem? Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from
>> the color LUT file. But, the issue is that I chose the label files from
>> that LUT file too. It meas the source that I chose the label files from 
>> and
>> the source of the region's names in tksurfer are the same. The problem is
>> just I do not have the label's names I merged to create annot file, in 
>> the
>> tksurfer GUI. It shows another names of that list! So, what do you think
>> about? What is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > > wrote:
>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open
>>> this annot file in tksurfer and click on colored regions which 
>>> corresponded
>>> to specific labels I had chosen them, I do not have their name on the
>>> vertex information part at the bottom of tksurfer GUI. It shows very
>>> different names for these regions. May you explains me what is the 
>>> problem
>>> I could not see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>>
>>
>>
>

>>>
>>
>
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Re: [Freesurfer] Very urgent matlab command line to transform vol to label.

[Douglas N Greve]

Try using this instead:
mri_binarize --i file_created_by_vol_2_surf.mgz --min threshold --o 
bin.file_created_by_vol_2_surf.mgz
mri_cor2label --i bin.file_created_by_vol_2_surf.mgz --id 1 ---l 
yourlabel.label

On 02/27/2016 06:28 AM, std...@virgilio.it wrote:
> Hi list,
> I have read on your mail list that I could use the command line 
> reported below to covert vol to label.
> I'm confused on the matlab command line.
> Specifically, if I using an MRS voxel (in native space or MNI, as 
> preferred) located bilaterally of 3.0x3.0x3.0 mm, which are *lindex, 
> lxyz, ovals?*
>
> v = load_mgh('file_created_by_vol_2_surf.mgz');
> ind = find(v > threshold);
> write_label(ind-1, [], v(ind), 'label_file_want_to_create');
> Thanks,
> Stefano
>
>
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Re: [Freesurfer] Map label from lh to rh

[Douglas N Greve]

It does not. You can run  mris_left_right_register. You will need to use 
mris_apply_reg instead of mri_label2label. See below. run with --help to 
get docs

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg

On 02/25/2016 04:28 PM, Makaretz, Sara Johanna wrote:
> Hi, I want to map a label from one hemi to the other (all on 
> fsaverage). I tried mri_label2label:
>
> mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel 
> lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface
>
> but I think I need to specify a reg file to go between hemispheres, 
> does this exist somewhere? an error message kindly pointed out that 
> this one does not exist: 
> /usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg
>
>
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

can you send your command line and terminal output?

On 02/25/2016 01:52 PM, Jennifer Legault wrote:
> Hi Douglas,
>
> Thank you for all your help.  When I say "volume" I do mean the FS 
> thickness*area measure.  I ran the mri_glmfit with --osgm and for the 
> FWHM received the value of .925737. Assuming that this rounds up to 1, 
> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to 
> find the CSD file and I selected the fwhm01 csd file.
>
> I then ran the mri_surfcluster command, however, I got the following 
> error:
>
> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
> CSD file was created with fsaverage
>
> Any suggestions you have would be appreciated.
>
> Best,
>
> Jen
>
> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve 
> > wrote:
>
> by "volume" do you mean a VBM-type analysis or do you mean the volume
> that comes out of FS (thickness*area)? If you are going to use a
> clusterwise correction, then you have to have a FWHM measurement. You
> can try analyzing it in mri_glmfit with --osgm just to get the
> FWHM out
> of it.
>
> You should be able to output a .mgh file instead of a .w file
>
>
> On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> > That's very useful, thank you.  In terms of FWHM, I am examining
> gray
> > matter volume, not cortical thickness, and was previously instructed
> > by Martin Reuter not to smooth these data.  Do you think it
> would make
> > sense then to just use the fwhm01?  And in terms of the voxel-wise
> > threshold, is there a commonly used value for GM volume data?  I am
> > still new to freesurfer and I appreciate any feedback.
> >
> > For visualization, after I run the mri_surfcluster the only outputs
> > are a summary file and a .w file, and freeview doesn't accept this
> > format.  Is it possible to have a cluster-wise corrected map (a
> > sig.cluster.mgh file) as they do for the Clusterwise Correction for
> > Multiple Comparisons tutorial here
> >
> ?
> >
> >
> > Best,
> >
> > Jen
> >
> > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
> > 
>  >> wrote:
> >
> >
> >
> > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > > Thank you for your response.  Do I need to run the glm_fit-sim
> > command
> > > to make the csd file?  I feel this would be inappropriate
> for my
> > data
> > > since I already ran the LME model.
> > No, look in
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> > need the FWHM though
> > >
> > > Second, is there an argument to make an output file that
> can be
> > > visualized via freeview?  In other words, how can I view
> my cluster
> > > thresholded data?
> > You can use freeview, something like
> > freeview -f lh.inflated:overlay=sig.mgh
> > There are other options for loading annotations and
> curvature. See the
> > freeview help
> > >
> > > Your help is greatly appreciated,
> > >
> > > Jen
> > >
> > >
> > >
> > > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > >  
> >
> > 
> >   > >
> > > There is a (very long) command line on that page. Mainly you
> > need
> > > a csd file. To get that you need the FWHM of your
> analysis, the
> > > voxel-wise threshold, and the sign of the contrast (or
> abs).
> > Then
> > > the relevant output will be the --sum. You can run it with
> > --help
> > > to get more info.
> > >
> > >
> > > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> > >> Thank you very much for your help! I still received a
> "cannot
> > >> read file type" error when I only added the path to
> the output
> > >> --o part, however when I also added the path to the
> input file,
> > >> it worked!
> > >>
> > >> I do have one more question: Which argument can I add so
> > that in
> > >> my output file I see the clusterwise P value, like it
> is shown
> > >> here
> > >>
> > 
> 
> 

Re: [Freesurfer] Fwd: View several Annot files in Tksurfer

[Douglas N Greve]

you cannot load more than one in tksurfer. You can load load more than 
one in freeview. As Bruce points out, you cannot visualize more than one 
at a time (unless you mean the outline?)

On 02/25/2016 06:06 PM, Bruce Fischl wrote:
> Hi Faezeh
>
> the annotations label every vertex. How would you view more than one 
> at the same time?
>
> cheers
> Bruce
> On Wed, 24 Feb 2016, Faeze Vedaei wrote:
>
>> Hi Freesurfer Experts,
>> In order to view specific annot files by tksurfer in Freesurfer, I used
>> mris_label2annot command to create annot files based on Destrieux atlas.
>> Now, I can import annot file in tksurfer, but just one file at the 
>> time. My
>> aim is to view several annot files by their specific colors in tksurfer
>> simultaneously. May you help me how can I do this? In advance, I'd
>> appreciate your consideration.
>>
>> Regards,
>> Faezeh Vedaei
>>
>>
>>
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

yes, just follow the pattern of the file. You will probably want to
use different RGB values to get different colored labels.

hth
d

On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  wrote:
> Hi,
>
> I should let you know that, it works! It shows paracentral name in tksurfer.
> So, how I have to revise my .ctab file to get the right result?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you for your response. I just used the command you suggested to use
>> by just a change in calling .ctab LUT file. I used the path:
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>> opinion?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>>
>>> Here is the text format of those files.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>>> wrote:

 Hi

 Thank you so much for your response. I attached here three files
 including the command lines, LUT file , and the list of names I want to get
 and what the result is actually. I'd appreciate if you look at them and let
 me know what is wrong with that.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but the
> result has not changed. Can you help me more how I can fix this problem?
> Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from
>> the color LUT file. But, the issue is that I chose the label files from 
>> that
>> LUT file too. It meas the source that I chose the label files from and 
>> the
>> source of the region's names in tksurfer are the same. The problem is 
>> just I
>> do not have the label's names I merged to create annot file, in the 
>> tksurfer
>> GUI. It shows another names of that list! So, what do you think about? 
>> What
>> is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open 
>>> this
>>> annot file in tksurfer and click on colored regions which corresponded 
>>> to
>>> specific labels I had chosen them, I do not have their name on the 
>>> vertex
>>> information part at the bottom of tksurfer GUI. It shows very different
>>> names for these regions. May you explains me what is the problem I 
>>> could not
>>> see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>
>>
>

>>>
>>
>
>
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] -qcache of v5.0 data with newer versions

[Douglas N Greve]

Yes
doug

On 02/23/2016 03:00 PM, Daniel Ferreira wrote:
> Dear experts,
>
> Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been 
> recon-all -all with FS 5.0.0?
>
> Thanks
>
> Dani
>
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] running two versions of fs in the same dataset

[Fengji Geng]

Dear fs developers,

we are attempting to use the stable version of fs 5.1 for processing while also 
using the most current version for hippocampal segmentation on the same set of 
subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop 
version of fs 6 was installed, we began having an issue with the fsaverage 
folder linking to the newest version, when we need it to link to version 5.1 
during processing. The label files that we need for processing in version 5.1 
are not accessible in the new version’s fsaverage folder. However, before we 
updated to fs 6.0 dev version on 28-Jan-2016, we never had this issue. So, we 
are wondering if the newest develop version of fs 6.0 does not allow two 
versions of fs to be used in the same data.

Looking forward to hearing from you and thanks in advance.

Best,

-
Fengji

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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

I should let you know that, it works! It shows paracentral name in
tksurfer. So, how I have to revise my .ctab file to get the right result?

Regards,
Faezeh Vedaei

On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  wrote:

> Hi,
>
> Thank you for your response. I just used the command you suggested to use
> by just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file
> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to get
>>> and what the result is actually. I'd appreciate if you look at them and let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 I checked again to arrange the labels in the order of LUT file, but the
 result has not changed. Can you help me more how I can fix this problem?
 Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> Thank you for your response. Yes, you are right. The names come from
> the color LUT file. But, the issue is that I chose the label files from
> that LUT file too. It meas the source that I chose the label files from 
> and
> the source of the region's names in tksurfer are the same. The problem is
> just I do not have the label's names I merged to create annot file, in the
> tksurfer GUI. It shows another names of that list! So, what do you think
> about? What is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open
>> this annot file in tksurfer and click on colored regions which 
>> corresponded
>> to specific labels I had chosen them, I do not have their name on the
>> vertex information part at the bottom of tksurfer GUI. It shows very
>> different names for these regions. May you explains me what is the 
>> problem
>> I could not see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>>
>
>

>>>
>>
>
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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Douglas N Greve]

try now

On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>
> Hi,
>
> I am having the same issue.
>
> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>
> Thanks a lot, Amelia
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
> Greve
> *Sent:* Wednesday, February 10, 2016 10:58 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> what is your command line? I think there is a rescaling in which it 
> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the 
> (siemens) scanner. Could that be the problem?
>
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>
> I ran into the same issue:
>
> FSLVersion 5.0.4
>
> FSLVerMaj 5
>
> FSL Version is 5.0.4, must be 3.X or 4.X
>
> I downloaded the epidewarp.fsl script from the suggested ftp site
> and replaced the existing script.  It did indeed fix the version
> incompatibility with FSL 5.x.
>
> I ran into a new problem where it was aborting.  After some
> trouble shooting and looking over the documentation, I realized
> that —-epi is a required input without which the script crashes
> (or is it supposed to be optional but there is a bug in the script?).
>
> After including it, it ran much further but then aborted with the
> following error:
>
> ERROR: input phase image exceeds allowable phase range.
>
> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>
> This is consistent with the documentation.  I’m not sure why the
> phase image exceeds the range though.
>
> It ran without problems with SPM’s FieldMap Toolbox and it is from
> a standard Siemen’s scanner sequence (two magnitude files and one
> phase difference file).
>
> Do I just divide the values by two with something like fslmaths
> since it seems to have exactly double the required range?
>
> Joe
>
> On Nov 26, 2014, at 21:36, Douglas Greve
> >
> wrote:
>
>
> It is there again. I don't know what the status if it  is in
> terms of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp
> site? I don’t see it at the link in the archives:
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I
> can the old script just be changed to accept 5.x version
> numbers.
>
> Cheers,
>
> -Morgan
>
> ___
> 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.
>
> 
> 
>
> Joseph Dien, PhD
>
> Senior Research Scientist
>
> Maryland Neuroimaging Center
>
> University of Maryland, College Park
>
> E-mail: jdie...@mac.com 
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
>
>
> ___
>
> Freesurfer mailing list
>
> Freesurfer@nmr.mgh.harvard.edu 
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Problem Installing FS

[Z K]

Odd. It should work so long as there is a "license.txt" file or 
".license" file. Just for the sake of trying, what happens if you copy 
the "license.txt" file to ".license" so that you have both?

   $> cd /Applications/freesurfer
   $> cp license.txt .license

And then try?

-Zeke

On 03/01/2016 02:13 PM, Millan, Carlos wrote:
> Hi Zeke,
>
> I do have a file named license.txt in my FREESURFER_HOME directory as
> well as another one named LICENSE that comes with the FS installation.
>
> When I type:
>
>   $> cd /Applications/freesurfer
>   $> ls -l license.txt
>
> What happens is this:
>
> -rw-r--r--@ 1 carlosmillan  staff  55 Feb 26 12:25 license.txt
>
>
> Does it mean I already have the license installed but I do not have
> administrator privileges and that’s why I’m not able to run FS? At this
> point I’m calling IT here at UM to see if that’s the problem, which is
> possible because it is not allowing me to use “sudo” either and the
> system says “sorry” after typing my password.
>
>
> Thanks,
>
>
> Carlos
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Please run the exact commands including the file I attached, not the
aparc.annot.a2009s.ctab, and check the result using the freeview
command I provided. Then let me know what label freeview shows.

hth
d

On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. I just used the command you suggested to use by
> just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to get
>>> and what the result is actually. I'd appreciate if you look at them and let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I checked again to arrange the labels in the order of LUT file, but the
 result has not changed. Can you help me more how I can fix this problem?
 Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> Thank you for your response. Yes, you are right. The names come from
> the color LUT file. But, the issue is that I chose the label files from 
> that
> LUT file too. It meas the source that I chose the label files from and the
> source of the region's names in tksurfer are the same. The problem is 
> just I
> do not have the label's names I merged to create annot file, in the 
> tksurfer
> GUI. It shows another names of that list! So, what do you think about? 
> What
> is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open 
>> this
>> annot file in tksurfer and click on colored regions which corresponded to
>> specific labels I had chosen them, I do not have their name on the vertex
>> information part at the bottom of tksurfer GUI. It shows very different
>> names for these regions. May you explains me what is the problem I could 
>> not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>

>>>
>>
>
>
> ___
> 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.
>
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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Versace, Amelia]

Hi,
I am having the same issue.
Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
Thanks a lot, Amelia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Wednesday, February 10, 2016 10:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x

what is your command line? I think there is a rescaling in which it expcts the 
phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) scanner. 
Could that be the problem?

On 2/10/16 10:40 PM, Joseph Dien wrote:
I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced 
the existing script.  It did indeed fix the version incompatibility with FSL 
5.x.

I ran into a new problem where it was aborting.  After some trouble shooting 
and looking over the documentation, I realized that --epi is a required input 
without which the script crashes (or is it supposed to be optional but there is 
a bug in the script?).

After including it, it ran much further but then aborted with the following 
error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I'm not sure why the phase image 
exceeds the range though.

It ran without problems with SPM's FieldMap Toolbox and it is from a standard 
Siemen's scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems 
to have exactly double the required range?

Joe

On Nov 26, 2014, at 21:36, Douglas Greve 
> wrote:


It is there again. I don't know what the status if it  is in terms of the 
version. Try it and let me know
doug
On 11/25/14 4:34 PM, Morgan Hough wrote:
Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I don't see it at 
the link in the archives:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old script just 
be changed to accept 5.x version numbers.

Cheers,

-Morgan

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Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com





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[Freesurfer] Problem Installing FS

[Millan, Carlos]

Hi Zeke,

I do have a file named license.txt in my FREESURFER_HOME directory as well as 
another one named LICENSE that comes with the FS installation.

When I type:

 $> cd /Applications/freesurfer
 $> ls -l license.txt

What happens is this:


-rw-r--r--@ 1 carlosmillan  staff  55 Feb 26 12:25 license.txt


Does it mean I already have the license installed but I do not have 
administrator privileges and that’s why I’m not able to run FS? At this point 
I’m calling IT here at UM to see if that’s the problem, which is possible 
because it is not allowing me to use “sudo” either and the system says “sorry” 
after typing my password.


Thanks,


Carlos
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

Thank you for your response. I just used the command you suggested to use
by just a change in calling .ctab LUT file. I used the path:
002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
calling aparc.annot.a2009s.ctab. It is strange that I created annot file
for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
opinion?

Regards,
Faezeh Vedaei

On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  wrote:

> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
> wrote:
>
>> Hi
>>
>> Thank you so much for your response. I attached here three files
>> including the command lines, LUT file , and the list of names I want to get
>> and what the result is actually. I'd appreciate if you look at them and let
>> me know what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but the
>>> result has not changed. Can you help me more how I can fix this problem?
>>> Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 Thank you for your response. Yes, you are right. The names come from
 the color LUT file. But, the issue is that I chose the label files from
 that LUT file too. It meas the source that I chose the label files from and
 the source of the region's names in tksurfer are the same. The problem is
 just I do not have the label's names I merged to create annot file, in the
 tksurfer GUI. It shows another names of that list! So, what do you think
 about? What is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
 wrote:

> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open
> this annot file in tksurfer and click on colored regions which 
> corresponded
> to specific labels I had chosen them, I do not have their name on the
> vertex information part at the bottom of tksurfer GUI. It shows very
> different names for these regions. May you explains me what is the problem
> I could not see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei
>


>>>
>>
>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

It works but the magic number now is  2067208 and read_surf still does not
read it

On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve 
wrote:

>
> try this version
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
>
> On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> > I changed the directory and it ran, but with errors. I had to change
> > the last part --surf lh.seghead --surf-smooth 10 because it does not
> > recognise --surf. When I change this to --o, it runs but with errors.
> >
> > On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve
> > > wrote:
> >
> >
> >
> > On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
> >> It seems to be giving me an error and saying it cannot read the
> >> seghead.mgz file.
> > Is it in the same directory where you are running the command? If
> > so, what is the terminal output?
> >>
> >> From my earlier question; do you know how to check if lh.seghead
> >> is corrupted?
> > If you can view it in tksurfer/freeview, then it is probably not
> > corrupted. I vaguely remember that there was some problem reading
> > this file in matlab, but I don't remember every coming up with a fix
> >
> >>
> >> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
> >> >
> wrote:
> >>
> >> you can try
> >>
> >> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
> >> --surf-smooth 10
> >>
> >>
> >>
> >>
> >> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
> >>> Is it possible to use a different function? Can I use
> >>> mri_vol2surf on the seghead.mgz file? Or do you think that
> >>> mkheadsurf is the right one to be using?
> >>>
> >>> Thanks!!
> >>>
> >>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> >>>  >>> > wrote:
> >>>
> >>> Can you load it in tksurfer or freeview?
> >>>
> >>>
> >>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>  Hi FreeSurfer users,
> 
>  I have used the "mkheadsurf" command to create a head
>  surface for my subject. However when I try to use
>  "read_surf" to read the "lh.seghead" file that is
>  created, the magic number is not one that is recognised.
> 
>  Having read some previous posts/questions with similar
>  problem/error, I think the problem is probably within
>  the "lh.seghead" file. I think someone wrote that
>  incompatibility of the magic number means that the
>  surface is corrupted. Is there a way to check errors of
>  mkheadsurf? Or whether something is wrong? It looked
>  fine in freeview.
> 
>  Does anybody have any advice?
> 
>  Thanks,
> 
>  Maheen
> 
> 
>  ___
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>  
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
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> >>> 
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> The information in this e-mail is intended only for the
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> >>> contains patient information, please contact the
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> >>> but does not contain patient information, please contact
> >>> the sender and properly
> >>> dispose of the e-mail.
> >>>
> >>>
> >>>
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> >>
> >>
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> >>
> >>
> >> The information in this e-mail is intended only for the
> >> person 

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

It is strange that the LUT file you sent doesn't seem to be named
anything similar to the file you called. You are calling

new/002_S_0413/labels/aparc.annot.a2009s.ctab

There also seem to be some basic issues with the command --s should
just have the name of the subject not a separate directory as well.

Why are you using the --nhits option?

Here is an example, of what I think is closer to what you want:

mris_label2annot --s 002_S_0413 --h lh --ctab faezeh_lut.ctab --a
myaparc_test --l 002_S_0413/labels/lh.G_and_S_paracentral.label

Work from there and see if that gets you the first one, then just add
as you go. Also check that you are properly loading the data in
freeview:

freeview -f 002_S_0413/surf/lh.inflated:annot=lh.myaparc_test.annot


hth
d

On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  wrote:
> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  wrote:
>>
>> Hi
>>
>> Thank you so much for your response. I attached here three files including
>> the command lines, LUT file , and the list of names I want to get and what
>> the result is actually. I'd appreciate if you look at them and let me know
>> what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but the
>>> result has not changed. Can you help me more how I can fix this problem?
>>> Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. Yes, you are right. The names come from the
 color LUT file. But, the issue is that I chose the label files from that 
 LUT
 file too. It meas the source that I chose the label files from and the
 source of the region's names in tksurfer are the same. The problem is just 
 I
 do not have the label's names I merged to create annot file, in the 
 tksurfer
 GUI. It shows another names of that list! So, what do you think about? What
 is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
 wrote:
>
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open 
> this
> annot file in tksurfer and click on colored regions which corresponded to
> specific labels I had chosen them, I do not have their name on the vertex
> information part at the bottom of tksurfer GUI. It shows very different
> names for these regions. May you explains me what is the problem I could 
> not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei


>>>
>>
>
>
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> HelpLine at
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> dispose of the e-mail.
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faezeh_lut.ctab
Description: Binary data
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Re: [Freesurfer] Problem Installing Freesurfer

[Z K]

My guess is that pico did not actually save the license file because by 
default all directories under /Applications is protected. Which mean the 
"sudo" command is required.

Do you definitely have a file called license.txt (or .license) in your 
FREESURFER_HOME directory? What happens when you type the following in a 
terminal window?

   $> cd /Applications/freesurfer
   $> ls -l license.txt

-Zeke





On 03/01/2016 11:14 AM, Millan, Carlos wrote:
>
>
> Dear Freesurfer Team,
>
> I am a researcher here at University of Miami and recently downloaded
> Freesurfer to do Cortical Thickness analysis. Unfortunately, I have
> followed the installation steps very carefully as indicated on your web
> page but I do not know if there is a security issue on this Mac or what
> is it? But when I am trying to test freesurfer I get a message that says
> "license not found".
>
> I have tried to install the license by copying and pasting the license
> text I received (license.txt) into the $FREESURFER_HOME directory but it
> did not work; so I tried to write the commands “cd
> /Applications/freesurfer” and then “pico license.txt”. In the next
> window I also pasted the license and then I saved the changes in pico,
> but that did not work either.
>
> Is there anything else I should do?
>
> I am attaching some screenshots from the terminal. Maybe those help you
> assessing the problem.
>
> Thank you,
>
> Carlos Millan
> Research Assistant
> Epilepsy Division – Neurology Department
> University of Miami
>
>
>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,


Here is the text format of those files.

Regards,
Faezeh Vedaei

On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  wrote:

> Hi
>
> Thank you so much for your response. I attached here three files including
> the command lines, LUT file , and the list of names I want to get and what
> the result is actually. I'd appreciate if you look at them and let me know
> what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but the
>> result has not changed. Can you help me more how I can fix this problem?
>> Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from the
>>> color LUT file. But, the issue is that I chose the label files from that
>>> LUT file too. It meas the source that I chose the label files from and the
>>> source of the region's names in tksurfer are the same. The problem is just
>>> I do not have the label's names I merged to create annot file, in the
>>> tksurfer GUI. It shows another names of that list! So, what do you think
>>> about? What is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I open
 this annot file in tksurfer and click on colored regions which corresponded
 to specific labels I had chosen them, I do not have their name on the
 vertex information part at the bottom of tksurfer GUI. It shows very
 different names for these regions. May you explains me what is the problem
 I could not see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei

>>>
>>>
>>
>
mris_label2annot --s new/002_S_0413/ --h lh --ctab 
new/002_S_0413/labels/aparc.annot.a2009s.ctab --a MYAPARC2 --l 
new/002_S_0413/labels/lh.G_and_S_paracentral.label --l 
new/002_S_0413/labels/lh.G_and_S_subcentral.label --l 
new/002_S_0413/labels/lh.G_cingul-Post-ventral.label --l 
new/002_S_0413/labels/lh.G_Ins_lg_and_S_cent_ins.label --l 
new/002_S_0413/labels/lh.G_oc-temp_med-Parahip.label --l 
new/002_S_0413/labels/lh.S_calcarine.label --l 
new/002_S_0413/labels/lh.S_central.label --l 
new/002_S_0413/labels/lh.S_circular_insula_ant.label --l 
new/002_S_0413/labels/lh.S_circular_insula_inf.label --l 
new/002_S_0413/labels/lh.S_circular_insula_sup.label --l 
new/002_S_0413/labels/lh.S_interm_prim-Jensen.label --l 
new/002_S_0413/labels/lh.S_oc_sup_and_transversal.label --l 
new/002_S_0413/labels/lh.S_oc-temp_lat.label --nhits nhits.mgh
The regions I am looking for:
* lh.S_oc-temp_lat.label
* lh.S_oc_sup_and_transversal.label
* lh.S_central.label
* lh.S_circular_insula_inf.label
* lh.G_oc-temp_med-Parahip.label
* lh.S_circular_insula_ant.label
* lh.S_interm_prim-Jensen.label
* lh.G_Ins_lg_and_S_cent_ins.label
* lh.G_and_S_subcentral.label
* lh.G_cingul-Post-ventral.label
* lh.S_calcarine.label
* lh.G_and_S_paracentral.label
* lh.S_circular_insula_sup.label

And the regions I got in tksurfer:
* Cingual_post_dorsal
* G_and_transv_frontc
* Front_inf_opecular
* Cuneus
* G_and_S_occipital_inf
* G_and_S_cingul_Ant
* G_front_inf_orbital
* G_and_S_paracentral


  0  Unknown   0   0   00
  1  G_and_S_frontomargin 23 220  600
  2  G_and_S_occipital_inf23  60 1800
  3  G_and_S_paracentral  63 100  600
  4  G_and_S_subcentral   63  20 2200
  5  G_and_S_transv_frontopol 13   0 2500
  6  G_and_S_cingul-Ant   26  60   00
  7  G_and_S_cingul-Mid-Ant   26  60  750
  8  G_and_S_cingul-Mid-Post  26  60 1500
  9  G_cingul-Post-dorsal 25  60 2500
 10  G_cingul-Post-ventral60  25  250
 11  G_cuneus180  20  200
 12  G_front_inf-Opercular   220  20 1000
 13  G_front_inf-Orbital 140  60  600
 14  G_front_inf-Triangul180 220 1400
 15  G_front_middle  140 100 1800
 16  G_front_sup 180  20 1400
 17  G_Ins_lg_and_S_cent_ins  23  10  100
 18  G_insular_short 225 140 1400
 19  G_occipital_middle  180  60 1800
 20  G_occipital_sup  20 220  600
 21  G_oc-temp_lat-fusifor60  20 1400
 22  G_oc-temp_med-Lingual   220 180 1400
 23  G_oc-temp_med-Parahip65 100  200
 24  G_orbital   220  60  200
 25  G_pariet_inf-Angular 20  60 2200
 

Re: [Freesurfer] AAL atlas question

[Makaretz, Sara Johanna]

I'm actually wondering the same thing re AAL to subject space - this is what I 
have been using:

spmregister - reg template to subject
mri_label2vol - move AAL to subject space
mri_segstats - pull in-volume stats using AAL in subject space
mri_vol2surf - project AAL (subject space) to subject surface
mris_anatomical stats - pull surface stats

Am I making that more complicated than it needs to be? What I'm most unsure 
about is whether the atlas should be projected to the template surface then 
moved to subject surface, or if it should be moved to subject space then 
projected to surface.

Thanks!
Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of 
pfot...@nmr.mgh.harvard.edu [pfot...@nmr.mgh.harvard.edu]
Sent: Monday, February 29, 2016 18:37
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] AAL atlas question

Hi FS community,

I have recon-ed a set of subjects and I was interested in also obtaining
structural info (cortical thickness, gray matter volume, surface area
etc.) based on a different atlas than the ones FS is using, and in
particular the AAL atlas.

I was wondering whether my approach would be the correct one or whether
there is another (better and more accurate) approach:

1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI
space into the native subjects' space,
2) Use mris_anatomical_stats to calculate the structural stats

Sorry for the potentially trivial question, and thank you for your time!

Best,
Panos

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[Freesurfer] Seeking postdoctoral candidates for datascience positions

[Satrajit Ghosh]

We are seeking two postdoctoral computational/data scientists with a PhD in
computer science, electrical or biomedical engineering, neuroscience,
statistics, or related fields to apply for positions in the McGovern
Institute for Brain Research at Massachusetts Institute of Technology.

The projects cover a broad array of neuroinformatics.

- Datamining of gene-behavior-anatomy relationships
- Architecting next generation dataflow systems
- Reproducible research platforms and applications
- Nonlinear image and other high-dimensional registration
- Predictive analytics in mental health
- Linked data platforms

Working on these projects will involve collaboration partners within and
across regional and international institutions. Candidates are expected to
develop algorithms and prototype ideas, contribute to opensource tools, and
perform software engineering, testing, and validation. Candidates will have
the opportunity to mentor undergraduate and graduate students, and
contribute to datascience at MIT.

The ideal candidates will have strong computational skills, enjoy
collaborating, and be able to adapt to and adopt a diverse set of
technologies. A documented PhD in computer science, electrical or
biomedical engineering, neuroscience, statistics, or related field is
required before starting this position. Positions are available for one
year, with a possibility of yearly extension depending on performance and
funding.

For inquiries please contact Satrajit Ghosh (sa...@mit.edu).
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

I still get the error option --surf unkown

On Mon, Feb 29, 2016 at 7:52 PM, Douglas N Greve 
wrote:

>
> try this version
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
>
> On 02/23/2016 10:17 AM, Maheen Siddiqui wrote:
> > I changed the directory and it ran, but with errors. I had to change
> > the last part --surf lh.seghead --surf-smooth 10 because it does not
> > recognise --surf. When I change this to --o, it runs but with errors.
> >
> > On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve
> > > wrote:
> >
> >
> >
> > On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
> >> It seems to be giving me an error and saying it cannot read the
> >> seghead.mgz file.
> > Is it in the same directory where you are running the command? If
> > so, what is the terminal output?
> >>
> >> From my earlier question; do you know how to check if lh.seghead
> >> is corrupted?
> > If you can view it in tksurfer/freeview, then it is probably not
> > corrupted. I vaguely remember that there was some problem reading
> > this file in matlab, but I don't remember every coming up with a fix
> >
> >>
> >> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve
> >> >
> wrote:
> >>
> >> you can try
> >>
> >> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
> >> --surf-smooth 10
> >>
> >>
> >>
> >>
> >> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
> >>> Is it possible to use a different function? Can I use
> >>> mri_vol2surf on the seghead.mgz file? Or do you think that
> >>> mkheadsurf is the right one to be using?
> >>>
> >>> Thanks!!
> >>>
> >>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> >>>  >>> > wrote:
> >>>
> >>> Can you load it in tksurfer or freeview?
> >>>
> >>>
> >>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>  Hi FreeSurfer users,
> 
>  I have used the "mkheadsurf" command to create a head
>  surface for my subject. However when I try to use
>  "read_surf" to read the "lh.seghead" file that is
>  created, the magic number is not one that is recognised.
> 
>  Having read some previous posts/questions with similar
>  problem/error, I think the problem is probably within
>  the "lh.seghead" file. I think someone wrote that
>  incompatibility of the magic number means that the
>  surface is corrupted. Is there a way to check errors of
>  mkheadsurf? Or whether something is wrong? It looked
>  fine in freeview.
> 
>  Does anybody have any advice?
> 
>  Thanks,
> 
>  Maheen
> 
> 
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> >>
> >> The information in this e-mail is intended only for the
> >> person to whom it is
> >> addressed. If 

Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[John Plass]

Hi Bruce,
When I run the last stage of the ex-vivo processing (recon-all -cortribbon
-sphere -surfreg -cortparc -parcstats -subjid $SUBID -noaseg), the
parcellation labels come out in the wrong place. I haven't been able to
figure out why this is happening, so I was wondering if its possible that
the surface registration is starting with the surface misoriented like it
is in tkmedit.

John


---
John Plass
Ph.D. Candidate
Visual Perception, Neuroscience, and Cognition Lab
Northwestern University

On Tue, Mar 1, 2016 at 7:38 AM, Bruce Fischl 
wrote:

> Hi John
>
> this is pretty puzzling. Is it causing any problems? tkmedit has been
> deprecated and it may just not be properly reading some header information
> or other. If nothing else is affected you can probably ignore it
>
> cheers
> Bruce
>
>
>
> On Mon, 29 Feb 2016, John Plass wrote:
>
> Hi Bruce,
>> Thanks for your help. In freeview, the surface outline overlays on the
>> volume correctly, and both the volume and the surface are oriented
>> correctly
>> in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented
>> correctly, but the surface appears to be oriented with some of the axes
>> swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of
>> the volume, but the outline of an axial slice of the surface, with the
>> anterior part pointing down.
>>
>> John
>>
>>
>>
>
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> is
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>
>
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[Freesurfer] "wm" boundaries and stats

[Krieger, Donald N.]

Freesurfer provides 34 ctx label volumes on each side of the brain with 
adjacent wm labels.
The boundary between each ctx volume and the co-named adjacent wm volume is a 
third "white" label.
I would like to extract a few pieces of information from the analogous boundary 
between each wm volume and those adjacent volumes to it which are not the 
co-named ctx volume.
For instance many wm volumes share a boundary with the unsegmented white matter.
Some share a boundary with sub-cortical structures.

Here are some of the information I would like to extract.
What do you think?

What are the xyz coordinates of the complete boundary surrounding each wm 
volume and what is the name of the adjacent volume for each point on the 
boundary?
I understand that for the boundary between the ctx volume and the adjacent wm 
volume, the white label provides this information.

What is the percentage and area of the complete boundary surrounding a wm 
volume which is adjacent to the co-named ctx volume.?

What are the names of the other volumes with which each wm volume shares a 
boundary and what is the percentage and area of the boundary shared with each?

For each point within a wm volume, are the nearest points on the wm boundary 
adjacent to the co-named ctx volume or are some adjacent to unsegmented white 
matter or sub-cortical structures?
More generally, is a particular few mm voxel surrounded by gray matter and so 
is likely primarily composed primarily of relatively short range fibers or is 
it adjacent to the deep white matter (unsegmented) and likely composed of a mix 
of relatively short range fibers and long range "en passage" fibers.
It is this last question which most closely gets at the ideas I wish to explore.
We are able to measure electric current in the white matter with mm resolution 
from the MEG.
The mix of local and "en passage" fibers should effect the direction of the 
electric currents in the white matter and I can measure that.
The distance scale is at the edge of that provided by DTI-derived tractography 
so we may be able to meld these measurements with those.

Your thoughts would be welcome on what is already there in freesurfer that will 
help with this and what you think might be a good direction to proceed to 
develop what we need from what is there.

Thanks - Don

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Re: [Freesurfer] ineffective skull strip

[Bruce Fischl]

Hi Lars

sure, if you can a better strip give it a try. Dura is really hard to get 
rid of , and depending on your bandwidth and readout direction you also can 
find fat shifting down to touch the edge of cortex


cheers
Bruce


On Tue, 1 Mar 2016, Lars M. Rimol wrote:



Hi,


We have run recon-all on 33 healthy subjects in their 20ies with FreeSurfer 
version 5.3.0, on a Linux CentOS 6.7. The original T1's look good 
(example image attached). We used the braindeer tool(http://brainder.org/201

1/09/10/quickly-inspect-freesurfer-cortical-surfaces/) to check the quality
 of the cortical reconstruction, and we find that in 10-15 subjects the cort
ical surface reconstruction was unsuccessful. We think it may 
have to do with an incomplete skull strip (please see attached images). In o
rder to get rid of residual dura (and some skull) we changed 
watershed first to 20 then to 5, using these commands:


1) recon-all -skullstrip -wsthresh 20 -clean-bm -subjid 
2) recon-all -autorecon-pial -subjid 
( We also tried: recon-all -skullstrip -clean-bm -multistrip -subjid   )

None of this changed the outcome much. Neither did -gcut .
An alternative is of course manual editing, but we are wondering whether usi
ng BEaST to do the skull strip, and then replacing the brainmask.mgz 
with the brainmasking resulting from BEaST (and then recon-all -autorecon-pi

al -subjid  ), could be a workable solution.
Would you recommend to do that/ not to do that?

Thank you!






sincerely yours,

Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway




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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview

[Bruce Fischl]

Hi John

this is pretty puzzling. Is it causing any problems? tkmedit has been 
deprecated and it may just not be properly reading some header information 
or other. If nothing else is affected you can probably ignore it

cheers
Bruce


On Mon, 29 Feb 2016, 
John Plass wrote:

> Hi Bruce,
> Thanks for your help. In freeview, the surface outline overlays on the
> volume correctly, and both the volume and the surface are oriented correctly
> in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented
> correctly, but the surface appears to be oriented with some of the axes
> swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of
> the volume, but the outline of an axial slice of the surface, with the
> anterior part pointing down.
> 
> John
> 
>
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[Freesurfer] Problem with brainstem substructures segmentation

[Riccardo Gubellini]

Dear Freesurfer users,

Sorry for reposting this message again, but I really need your help.

We have downloaded the Freesurfer 6.0 version since we are really
interested in the brainstem segmentation.
We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM.
We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7)
enabling  4vcpu 11Gb of RAM.
Disk space was 50 GB and after installation we have 15 GB free for data.

We have launched recon-all –all  for some cases and everything went right.
Then we have tried to launch recon-all –all –s nameofsunbject
–brainstem-structures
and the process, after about 6 hours, stacks, during  the SegmentSubject
process and after having computing hyperparameters for estimation of
Gaussian parameters.
Do you have any ideas of what is happening?

We tried to launch the brainstem segmentation also for the test data (
ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz) but
we still have the same problem.

Could it be a problem the use of a virtual machine Linux instead of real
Linux machine?

Thank you for your help.

Riccardo Gubellini
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