Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-11 Thread Ting Li 
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Dear Dr. Douglas,

Thank you so much for your response. With your instruction, it works. This is 
how I did. 

First, copy the significant cluster annot file from the simulation fold to one 
of subject label folder.
Secondly, use the mir_annotation2label command to make this cluster into a 
label file
Thirdly, copy this label file to fsaverage label folder
Finally, I can load the label to the fsaverage surf. 

Is this the right procedure? Thanks a lot!

Regards,
Ting
> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Which subject did you load it on? It must be fsaverage. Can you send the 
> terminal output and command line?
> 
> On 10/03/2018 11:31 PM, Ting Li wrote:
>> 
>> External Email - Use Caution
>> 
>> Dear Freesurfer Expert,
>> 
>> I have figured out the problem is that I didn’t specify lh before the 
>> annot file. However, in this method, I didn’t get the right label for 
>> I have loaded the label into the subject file. It is the scatter points.
>> 
>> I want to create label through mri_glm-fit-sim clusters. What command 
>> I should use? Please specify it for me. Thanks a lot!
>> 
>> Your help means a lot.
>> 
>> Regards,
>> Ting
>>> On Oct 3, 2018, at 9:38 PM, Ting Li >> >> wrote:
>>> 
>>> I have also tried the command without annot in specifying the 
>>> annotation file. Thanks a lot.
>>> 
>>> Regards,
>>> 
>>> Ting
 On Oct 3, 2018, at 9:36 PM, Ting Li >>>  
 >> wrote:
 
 Dear Freesurfer Experts,
 
 I really need your attention and help. Thanks a lot.
 
 We want to create label through the mri_glm-fit-sim cluster results.
 
 We have found the same topic in 2013 and tried the method you have 
 provided. However, it doesn’t work. If you think it is not the right 
 way, could you give me an example to do it right. I really 
 appreciate your great help. Thanks a lot.
 
 Here is my code:
 
 mri_annotation2label --subject F999  --hemi lh --annotation 
 cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
 
 Here is my error information:
 subject = F999
 annotation = cache.th20.neg.sig.ocn.annot
 hemi = lh
 labelbase = lh.test_label
 surface   = white
 
 Reading surface
  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
 Loading annotations from 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
 could not read annot file 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
 No such file or directory
 INFO: could not load from 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
  
 trying 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
 could not read annot file 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
 No such file or directory
 ERROR: MRISreadAnnotation() failed
 
 This is the annot files in my directory F999:
 ls F999/label/*.annot
 F999/label/cache.th20.neg.sig.ocn.annot 
 F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
 F999/label/lh.aparc.a2009s.annot 
 F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
 F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot 
 F999/label/rh.BA_exvivo.thresh.annot
 F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot
>>> 
>> 
>> 
>> 
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Re: [Freesurfer] mri_watershed Error

2018-10-11 Thread Bruce Fischl 

Hi Boris

the input to that watershed call is the T1.mgz, but it is already 
problematic as you can see from the log. You should take a look at the 
nu.mgz and make sure it is correct. You can also email me the nu.mgz and 
the talairach.xfm (in the mri/transforms dir) if you want and I'll take a 
look

cheers
Bruce


On Thu, 11 Oct 2018, Boris 
Rauchmann wrote:


   External Email - Use Caution 


Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the 
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[Freesurfer] Postdoctoral position open to work on brain MRI function & microstructure (Italy)

2018-10-11 Thread Jovicich, Jorge 
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[Apologies for cross-posting]

The MRI Group of the Center for Mind/Brain Sciences, University of 
Trento, Italy  (https://r.unitn.it/en/cimec/mri/) has an open 
postdoctoral position to develop/apply MRI acquisition and analyses 
methods to characterize structural and dynamic functional  connectivity 
(deadline October 30, 2018).

More information about our group, the call and application links can be 
found here:
https://r.unitn.it/en/cimec/mri/opportunities

Feel free to distribute this announcement to potentially interested people.

Best,

     Jorge Jovicich

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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Re: [Freesurfer] mri_watershed Error

2018-10-11 Thread Boris Rauchmann 
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Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the 
input to watershed.  

recon-all.log
Description: Binary data


Thanks,
Boris

> Am 11.10.2018 um 18:55 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you check to make sure that the input to the watershed looks ok? Also, in 
> general it is a lot easier for us to help if you send us the full command 
> line and screeen output and attach the recon-all.log
> 
> cheers
> Bruce
> 
> 
> On Thu, 11 Oct 2018, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> When I run recon-all i get the follwing error message:
>>  mri_watershed Error: 
>>  GLOBAL region of the brain empty !
>> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
>> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>> The .nii file looks fine. Can someone help me with this? 
>> Best,
>> Boris
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[Freesurfer] FreeSurfer Errors

2018-10-11 Thread Sparsh Jain 
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Hey!

I have recently started using FreeSurfer. I have encountered multiple
errors over the past few days, and I would like to mention them all.

1. While testing the installation, the code ran for roughly 4-6 hours and
generated the T1 and wm output images. The brainmask image failed to load
even after multiple attempts.
2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM
images (about 120-145 images). Running dcmunpack on the directory to locate
the suitable T1 weighted image (to pass as the input image to freesurfer)
returns an error message 'Element not found'. It fails to generate a list
of usable input images. The log file also only mentions the error message.
Basically, I am having trouble working with DICOM images using Freesurfer.
Please advise me on how to go about it.
3. I tried using the dcm2nii tool on the DICOM images. The software gave
out three (nearly identical) nii.gz files as output, each about 7 MB in
size. I tried running reconstruction on all three one by one. Only the
'compressed' version output underwent reconstruction for a long time
without giving any errors. However, the reconstruction process went on for
150 hours without completion. There were no errors during this time, and
the mris_fix_topo process went on for about 74 hours until tonight. It was
working on 'correcting defect 48' for most of this time, and then the PC
suddenly stopped responding. The process had been utilizing 100% of the CPU
and 87% of the RAM for a long time, but the computer was always responding.
However it suddenly stopped responding after about 74 hours of
mris_fix_topology process. My machine has 8 GB RAM and more than 3.4 GHz
processing speed (Acer Veriton).
4. Previously, I tried running reconstruction on a different subject's data
after converting it to nifti using dcm2niix. After 70 hours of execution,
it terminated with an error which showed that the fsaverage folder was
inaccessible. Further digging revealed that the folder  was somehow
pointing to itself. The original error said failed to read from the label
file.
 I had to eventually reinstall FreeSurfer.
5. I tried running iElvis pipeline. After some time I got an error which
said that the sphere.reg file couldn't be opened. I tried fixing this but
nothing worked. I kept getting the error that lh.sphere.reg file could not
be opened and so on.

Please help. I have been trying to run it for weeks now. I hope you will be
able to address each of these problems soon.

Thank You

Sparsh
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Re: [Freesurfer] Correction Needed for the Midline

2018-10-11 Thread Diamond, Bram Ryder 
Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
 midline cutting error, that
 is the midline does not go through exactly the center of the brain in 
 coronal cut. For example, the
 midline is a little bit fuzzy and goes through an hemisphere than the 
 other (see attachment). I've
 searched in the mail list and ​I don't find the way to fix it. Does anyone 
 have any idea to fix it?
 Thank you,
 Maxime Perron
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Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

2018-10-11 Thread ece ulug 
External Email - Use Caution


I tried to confirm VBM analysis lots of platform i study in CAT, these days. 
Thanks for your reply. 


Greve, Douglas N.,Ph.D.  şunları yazdı (11 Eki 2018 
18:47):

> Which template surface? fsaverage? Are you using the 2mm MNI template 
> for VBM?  If so, then you can use mri_label2vol specifying the desikan 
> annotation as the --annot and using 
> $FREESURFER_HOME/average/mni152.register.dat as the registration file.
> 
>> On 10/11/2018 11:42 AM, ece ulug wrote:
>> 
>> External Email - Use Caution
>> 
>> Thanks for your response;
>> 
>> 
>> I had already mapped normalized volume to template surface, so now I 
>> want to map the desikan atlas into the vbm volume.
>> 
>> 
>> 
>> 
>> *Gönderen:* Greve, Douglas N.,Ph.D.  adına 
>> freesurfer-boun...@nmr.mgh.harvard.edu 
>> 
>> *Gönderildi:* 11 Ekim 2018 Perşembe 18:26
>> *Kime:* freesurfer@nmr.mgh.harvard.edu
>> *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space
>> I'm not sure what you are trying to do. Do you want to map the vbm
>> results to the surface and visualize the aparc (desikan atlas) or do you
>> want to map the aparc into the vbm volume?
>> 
>>> On 10/11/2018 09:59 AM, ece ulug wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> Hi,
>>> 
>>> May be i cannot tell well,
>>> 
>>> 
>>> I would like to use the Desikan atlas, which is a surface-based atlas
>>> normally, as a volume template.
>>> 
>>> Generally Desikan_surface.gii file is accesible. Can I visualize VBM
>>> results correctly in for instances SPMglass brain using Desikan 
>> Atlas.nii?
>>> 
>>> 
>>> Ece
>>> 
>>> 
>>> 
>>> *Gönderen:* ece ulug 
>>> *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
>>> *Kime:* freesurfer@nmr.mgh.harvard.edu
>>> *Konu:* Desikan Atlas in MNI Space
 /Dear All,/
 /
 I am a master student in Turkey. For my thesis; I have to do exactly
 this;
 
 /
 /*Desikan atlas (which I have in the tailarach space) in the MNI
 space, as a file (Desikan_mni.nii). I am aware that transforming from
 one space to the other is not a very good idea but nevertheless I
 would like to test some computations.
 
 Anyone can attach/send a link/know of if exists such a file? the
 aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
 */
 /This is a mail dated 2014, freesurfer maillist, and I find this via
 internet./
 /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for
 these file? /
 /And what is your opinion, is it good idea? /
 /(To transform Desikan atlas to mni space for visualization VBM
 results?) /
 /Thanks in advance/
 /E. Ece Uluğ/
>>> 
>>> 
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>> Freesurfer Info Page - Harvard University 
>> 
>> mail.nmr.mgh.harvard.edu
>> To see the collection of prior postings to the list, visit the 
>> Freesurfer Archives.. A searchable archive which of messages PRIOR to 
>> March 2004 is at this site A searchable archive which includes 
>> messages AFTER March 2004 is at this site. Using Freesurfer
>> 
>> 
>> 
>> 
>> 
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Re: [Freesurfer] denoising and recon-all {Disarmed}

2018-10-11 Thread Lisa Crystal Krishnamurthy 
External Email - Use Caution

The ONLM denoising algorithm in the following package: 
(https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging)

Best,
-Lisa

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Glasser, Matthew
Sent: Thursday, October 11, 2018 12:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] denoising and recon-all


External Email - Use Caution
What are you using for denoising?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Lisa Crystal Krishnamurthy 
mailto:lkrishnamur...@gsu.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, October 11, 2018 at 11:05 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] denoising and recon-all


External Email - Use Caution
Hi,

I have found that denoising the MPRAGE prior to FS recon-all seems to improve 
the segmentation (see attached pdf). However, it is not clear if the denoising 
algorithm may cause some signal intensity changes (especially in voxels with 
partial voluming at the edge of the brain) that violate assumptions of 
recon-all. Could you help me understand what the assumptions of your algorithm 
are, and what I need to do to make sure my images conform to those assumptions?

Your help is greatly appreciated.
Best,
-Lisa


The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
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Re: [Freesurfer] mri_watershed Error

2018-10-11 Thread Bruce Fischl 

Hi Boris

can you check to make sure that the input to the watershed looks ok? Also, 
in general it is a lot easier for us to help if you send us the full 
command line and screeen output and attach the recon-all.log


cheers
Bruce


On Thu, 11 Oct 
2018, Boris Rauchmann wrote:




External Email - Use Caution

When I run recon-all i get the follwing error message:

 mri_watershed Error: 
 GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018

The .nii file looks fine. Can someone help me with this? 

Best,
Boris


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Re: [Freesurfer] denoising and recon-all

2018-10-11 Thread Glasser, Matthew 
External Email - Use Caution

What are you using for denoising?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Lisa Crystal Krishnamurthy 
mailto:lkrishnamur...@gsu.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, October 11, 2018 at 11:05 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] denoising and recon-all


External Email - Use Caution
Hi,

I have found that denoising the MPRAGE prior to FS recon-all seems to improve 
the segmentation (see attached pdf). However, it is not clear if the denoising 
algorithm may cause some signal intensity changes (especially in voxels with 
partial voluming at the edge of the brain) that violate assumptions of 
recon-all. Could you help me understand what the assumptions of your algorithm 
are, and what I need to do to make sure my images conform to those assumptions?

Your help is greatly appreciated.
Best,
-Lisa


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

2018-10-11 Thread Greve, Douglas N.,Ph.D. 
Which template surface? fsaverage? Are you using the 2mm MNI template 
for VBM?  If so, then you can use mri_label2vol specifying the desikan 
annotation as the --annot and using 
$FREESURFER_HOME/average/mni152.register.dat as the registration file.

On 10/11/2018 11:42 AM, ece ulug wrote:
>
> External Email - Use Caution
>
> Thanks for your response;
>
>
> I had already mapped normalized volume to template surface, so now I 
> want to map the desikan atlas into the vbm volume.
>
>
>
> 
> *Gönderen:* Greve, Douglas N.,Ph.D.  adına 
> freesurfer-boun...@nmr.mgh.harvard.edu 
> 
> *Gönderildi:* 11 Ekim 2018 Perşembe 18:26
> *Kime:* freesurfer@nmr.mgh.harvard.edu
> *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space
> I'm not sure what you are trying to do. Do you want to map the vbm
> results to the surface and visualize the aparc (desikan atlas) or do you
> want to map the aparc into the vbm volume?
>
> On 10/11/2018 09:59 AM, ece ulug wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > May be i cannot tell well,
> >
> >
> > I would like to use the Desikan atlas, which is a surface-based atlas
> > normally, as a volume template.
> >
> > Generally Desikan_surface.gii file is accesible. Can I visualize VBM
> > results correctly in for instances SPMglass brain using Desikan 
> Atlas.nii?
> >
> >
> > Ece
> >
> >
> > 
> > *Gönderen:* ece ulug 
> > *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
> > *Kime:* freesurfer@nmr.mgh.harvard.edu
> > *Konu:* Desikan Atlas in MNI Space
> >> /Dear All,/
> >> /
> >> I am a master student in Turkey. For my thesis; I have to do exactly
> >> this;
> >>
> >> /
> >> /*Desikan atlas (which I have in the tailarach space) in the MNI
> >> space, as a file (Desikan_mni.nii). I am aware that transforming from
> >> one space to the other is not a very good idea but nevertheless I
> >> would like to test some computations.
> >>
> >> Anyone can attach/send a link/know of if exists such a file? the
> >> aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
> >> */
> >> /This is a mail dated 2014, freesurfer maillist, and I find this via
> >> internet./
> >> /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for
> >> these file? /
> >> /And what is your opinion, is it good idea? /
> >> /(To transform Desikan atlas to mni space for visualization VBM
> >> results?) /
> >> /Thanks in advance/
> >> /E. Ece Uluğ/
> >
> >
> > ___
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[Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

2018-10-11 Thread ece ulug 
External Email - Use Caution

Thanks for your response;


I had already mapped normalized volume to template surface, so now I want to 
map the desikan atlas into the vbm volume.



Gönderen: Greve, Douglas N.,Ph.D.  adına 
freesurfer-boun...@nmr.mgh.harvard.edu 
Gönderildi: 11 Ekim 2018 Perşembe 18:26
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space

I'm not sure what you are trying to do. Do you want to map the vbm
results to the surface and visualize the aparc (desikan atlas) or do you
want to map the aparc into the vbm volume?

On 10/11/2018 09:59 AM, ece ulug wrote:
>
> External Email - Use Caution
>
> Hi,
>
> May be i cannot tell well,
>
>
> I would like to use the Desikan atlas, which is a surface-based atlas
> normally, as a volume template.
>
> Generally Desikan_surface.gii file is accesible. Can I visualize VBM
> results correctly in for instances SPMglass brain using Desikan Atlas.nii?
>
>
> Ece
>
>
> 
> *Gönderen:* ece ulug 
> *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
> *Kime:* freesurfer@nmr.mgh.harvard.edu
> *Konu:* Desikan Atlas in MNI Space
>> /Dear All,/
>> /
>> I am a master student in Turkey. For my thesis; I have to do exactly
>> this;
>>
>> /
>> /*Desikan atlas (which I have in the tailarach space) in the MNI
>> space, as a file (Desikan_mni.nii). I am aware that transforming from
>> one space to the other is not a very good idea but nevertheless I
>> would like to test some computations.
>>
>> Anyone can attach/send a link/know of if exists such a file? the
>> aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
>> */
>> /This is a mail dated 2014, freesurfer maillist, and I find this via
>> internet./
>> /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for
>> these file? /
>> /And what is your opinion, is it good idea? /
>> /(To transform Desikan atlas to mni space for visualization VBM
>> results?) /
>> /Thanks in advance/
>> /E. Ece Uluğ/
>
>
> ___
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University
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To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using Freesurfer





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Re: [Freesurfer] mri_watershed Error

2018-10-11 Thread Greve, Douglas N.,Ph.D. 
can you send the recon-all log file?

On 10/11/2018 11:22 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> When I run recon-all i get the follwing error message:
>
>  mri_watershed Error:
>  GLOBAL region of the brain empty !
> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 
> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>
> The .nii file looks fine. Can someone help me with this?
>
> Best,
> Boris
>
>
>
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Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space

2018-10-11 Thread Greve, Douglas N.,Ph.D. 
I'm not sure what you are trying to do. Do you want to map the vbm 
results to the surface and visualize the aparc (desikan atlas) or do you 
want to map the aparc into the vbm volume?

On 10/11/2018 09:59 AM, ece ulug wrote:
>
> External Email - Use Caution
>
> Hi,
>
> May be i cannot tell well,
>
>
> I would like to use the Desikan atlas, which is a surface-based atlas 
> normally, as a volume template.
>
> Generally Desikan_surface.gii file is accesible. Can I visualize VBM 
> results correctly in for instances SPMglass brain using Desikan Atlas.nii?
>
>
> Ece
>
>
> 
> *Gönderen:* ece ulug 
> *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
> *Kime:* freesurfer@nmr.mgh.harvard.edu
> *Konu:* Desikan Atlas in MNI Space
>> /Dear All,/
>> /
>> I am a master student in Turkey. For my thesis; I have to do exactly 
>> this;
>>
>> /
>> /*Desikan atlas (which I have in the tailarach space) in the MNI 
>> space, as a file (Desikan_mni.nii). I am aware that transforming from 
>> one space to the other is not a very good idea but nevertheless I 
>> would like to test some computations.
>>
>> Anyone can attach/send a link/know of if exists such a file? the 
>> aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
>> */
>> /This is a mail dated 2014, freesurfer maillist, and I find this via 
>> internet./
>> /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for 
>> these file? /
>> /And what is your opinion, is it good idea? /
>> /(To transform Desikan atlas to mni space for visualization VBM 
>> results?) /
>> /Thanks in advance/
>> /E. Ece Uluğ/
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] mri_watershed Error

2018-10-11 Thread Boris Rauchmann 
External Email - Use Caution

When I run recon-all i get the follwing error message:

 mri_watershed Error:
 GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018

The .nii file looks fine. Can someone help me with this?

Best,
Boris
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[Freesurfer] Ynt: Desikan Atlas in MNI Space

2018-10-11 Thread ece ulug 
External Email - Use Caution

Hi,

May be i cannot tell well,


I would like to use the Desikan atlas, which is a surface-based atlas normally, 
as a volume template.

Generally Desikan_surface.gii file is accesible. Can I visualize VBM results 
correctly in for instances SPMglass brain using Desikan Atlas.nii?

Ece



Gönderen: ece ulug 
Gönderildi: 10 Ekim 2018 Çarşamba 12:27
Kime: freesurfer@nmr.mgh.harvard.edu
Konu: Desikan Atlas in MNI Space

Dear All,

I am a master student in Turkey. For my thesis; I have to do exactly this;

Desikan atlas (which I have in the tailarach space) in the MNI space, as a file 
(Desikan_mni.nii). I am aware that transforming from one space to the other is 
not a very good idea but nevertheless I would like to test some computations.

Anyone can attach/send a link/know of if exists such a file? the aparc+aseg.mgz 
in fsaverage is in mni305 space. will that work?

This is a mail dated 2014, freesurfer maillist, and I find this via internet.

Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for these 
file?

And what is your opinion, is it good idea?

(To transform Desikan atlas to mni space for visualization VBM results?)

Thanks in advance

E. Ece Uluğ

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Re: [Freesurfer] Recon-all with/without T2 give the same stats

2018-10-11 Thread Jianzhong Chen 
External Email - Use Caution

The aparc stats with T2 changed using this script. Now the stats
with/without T2 are different, thanks! It seems that in 5.3 the aparc stats
are computed before refining the pial.

Greve, Douglas N.,Ph.D.  于2018年10月11日周四 上午2:24写道：

> I think this was a bug in 5.3. Try running recon-all like
> recon-all -s subject -parcstats -parcstats2 -parcstats3
> to regenerate the stats files
>
> On 10/09/2018 11:19 PM, Jianzhong Chen wrote:
> >
> > External Email - Use Caution
> >
> > They are different. I attached two screenshots of lh.thickness
> > overlaying on lh.inflated here.
> >
> > Greve, Douglas N.,Ph.D.  > > 于2018年10月9日周二 下午10:22写道：
> >
> > But are the lh.thickness files the same or different?
> >
> > On 10/9/18 1:46 AM, Jianzhong Chen wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hi Dr. Greve,
> >>
> >> I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses
> >> (and the other measures like volume and area) are all the same.
> >>
> >> Thanks,
> >> Jianzhong
> >>
> >> Greve, Douglas N.,Ph.D.  >> > 于2018年10月9日周二 上午10:16写道：
> >>
> >> The aseg.stats should be the same since that does not make
> >> reference to the surfaces. The aparc stats should have been
> >> different because the thickness should have been different.
> >> Can you check whether the thickness files are different?
> >>
> >> On 10/8/18 9:39 AM, Jianzhong Chen wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Dear All,
> >>>
> >>> I tried recon-all with/without T2 image using FS 5.3.0. Then
> >>> I found that the aseg stats and aparc stats with/without T2
> >>> are exactly the same. When I check the pial surfaces, I can
> >>> see that they are very similar but not the same. So is it
> >>> reasonable to see exactly the same stats?
> >>> An example of the pial surfaces with/without T2 is attached
> >>> here. The red line is lh.pial with T2 and the yellow line is
> >>> the lh.pial without T2
> >>> My command for recon-all with T2 is: recon-all -s ${subject}
> >>> -i T1.nii -all -T2 T2.nii -T2pial -sd ${T2_dir}
> >>> My command for recon-all without T2 is: recon-all -s
> >>> ${subject} -i T1.nii -all -sd ${T1_dir}
> >>>
> >>> Thanks,
> >>> Jianzhong
> >>>
> >>>
> >>> ___
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Re: [Freesurfer] Difference between 2 mgh files in surf dir (or: effects of 'mri_surf2surf --prune' without smoothing)

2018-10-11 Thread ts+ml 
External Email - Use Caution

Looks like, it the output of that command is `diffcount 0`.

If you binary-diff them you see some differences near the start, but that's 
most likely just header info like creation time or something.

Ok, that answers my question. Thanks for your help!

Tim

> On October 10, 2018 at 8:13 PM "Greve, Douglas N.,Ph.D." 
>  wrote:
> 
> 
> I think they are probably the same thing. Can you run
> mri_diff lh.area.fsaverage.mgh lh.area.fwhm0.fsaverage.mgh
> 
> 
> 
> On 10/10/2018 11:12 AM, ts...@rcmd.org wrote:
> >  External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > what is the difference between the following 2 files found in a subject's 
> > surf/ directory:
> >* file #1: lh.area.fsaverage.mgh
> >* file #2: lh.area.fwhm0.fsaverage.mgh
> >
> >
> > I see in the logs (/scripts/recon-all.log), that file #2 is 
> > generated from file #1 by running the following command:
> >
> >  mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval 
> > lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex
> >
> > I know that if fwhm > 0, spatial smoothing will be applied. But what 
> > happens if fwhm is 0? From a quick comparison of the data in both files, 
> > they seem to be identical, but the hashes of the files differ. Is the 
> > difference only about the header?
> >
> > Thanks for your help,
> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> >
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] masking cortical thickness

2018-10-11 Thread N Saf 
External Email - Use Caution

Hi,

Thank you so much , it works.

BRG,
Nazanin

On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> if you want to mask the thickness, then use mri_mask
>
> On 10/10/2018 10:30 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglos,
> >
> > as you recommended, I used the --outmask and create the binary mask of
> > a label in mgh format. as I use the mri_binarize command with this
> > mask and ?h.thickness; the output is binary too or if I use --match
> > flag or --min --max flag the out put is 1 for those range, but I want
> > the thickness values on my mask, not 1 all over it , how should I do
> that?
> >
> > any detail information will be appreciated.
> >
> > BRG,
> > Nazanin
> >
> >
> > On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Use the --outmask option
> >
> > On 10/07/2018 08:59 AM, N Saf wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear Douglos,
> > >
> > > I did not understand how to use mri_label2label with the mask
> > > option(there is srcmask options not mask alone !). I extract my
> > labels
> > > and as you explained I wanted to create i.e. binary mask of
> > > rh.fusiform.label  with mri_label2label :
> > >   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
> > > --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface
> > > --hemi rh
> > >
> > > but it creats another label file not binary with mgh format I
> > did not
> > > get how can I create mybinary.mgh mask in order to use in third
> > > command "mri_binarize --i lh.thickness --mask youmask.mgh --o
> > > lh.thickness.masked.mgh"
> > >
> > > would you please help me with this, it would be a great favor.
> > >
> > > Best regards,
> > > Nazanin
> > >
> > > On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > > Yes, that should work. You can create a mask by breaking the
> > > annotation
> > > into labels (mri_annotation2label), then converting the
> > label into a
> > > binary mask (mri_label2label with --mask option), then
> > > mri_binarize --i
> > > lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
> > >
> > >
> > > On 07/30/2018 01:47 AM, N Saf wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear Freesurfer Experts,
> > > >
> > > > I wonder how can I show the cortical thickness surface on
> > just one
> > > > region of my interest in Freeview.  assume that I want to
> > see the
> > > > thickness surface of one of the regions in DKTatlas. does it
> > > work if I
> > > > make a binary mask of that specific region on
> > > aparcDKTatlas.annot and
> > > > then multiply it to the ?h.thickness surface ?? any help
> > will be
> > > > appreciated.
> > > >
> > > > Best Regards,
> > > > Nazanin
> > > >
> > > >
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