External Email - Use Caution        

 
Thanks for the quick reply!
 
When trying to run mri_vol2surf on my BOLD data, Freesurfer gives me an error because the thickness file does not match my other surf files. I have downsampled all other surf files using mris_decimate. However, I do not seem to be able to downsample the thickness file using mri_surf2surf (as it is missing a proper thickness file for reference) or mris_decimate. I would like to keep my data in native space, so it is not an option to resample the surface onto fsaverage.
 
What is the best way to go here? Is there another way to downsample the thickness file?
 
Cheers,
Ella
 
Gesendet: Freitag, 22. Februar 2019 um 22:34 Uhr
Von: freesurfer-request@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Freesurfer Digest, Vol 180, Issue 48
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Today's Topics:

1. Re: ?h.white does not exist (Bruce Fischl)
2. [All] postdoctoral position in PET imaging available at MGH /
Martinos Center (Bruce Fischl)
3. Re: ?h.white does not exist (Weber, Wade A)
4. Re: CAT12 surfaces on tkregister2 and Freeview
(Greve, Douglas N.,Ph.D.)
5. Re: ?h.white does not exist (Bruce Fischl)
6. Re: recon-all -hires (Greve, Douglas N.,Ph.D.)
7. Re: ?h.white does not exist (Greve, Douglas N.,Ph.D.)
8. Re: ?h.white does not exist (Weber, Wade A)
9. Re: ?h.white does not exist (Weber, Wade A)
10. downsampling orig.mgz (Ey Dude)
11. Re: recon-all -hires (Nasiriavanaki, Zahra)
12. Re: petsurfer Kinetic Modeling (MRTM1, MRTM2) (john Anderson)
13. Re: registration and resampling in native space
(Francesca Strappini)
14. Re: petsurfer Kinetic Modeling (MRTM1, MRTM2)
(Greve, Douglas N.,Ph.D.)
15. Re: registration and resampling in native space
(Greve, Douglas N.,Ph.D.)
16. vlrmerge for visualization only? (Haroon Popal)
17. Re: downsampling orig.mgz (Greve, Douglas N.,Ph.D.)
18. Re: vlrmerge for visualization only? (Greve, Douglas N.,Ph.D.)
19. Different paradigm files (Zhi Li)
20. Re: registration and resampling in native space
(Francesca Strappini)
21. Re: Different paradigm files (Greve, Douglas N.,Ph.D.)


----------------------------------------------------------------------

Message: 1
Date: Fri, 22 Feb 2019 12:57:59 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1902221257350.12350@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first
and see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

> External Email - Use Caution
>
> Hi Bruce,
>
> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.
>
> Wade
>
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:38 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> from the recon-all.log it looks like you never ran autorecon3. Is there a reason for this? Usually we run all the way through autorecon3 before running the T2pial stuff
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>
>>
>> ????????External Email - Use Caution
>>
>> Hi all,
>>
>> ?
>>
>> I?m trying to run ?autorecon2 on 3 subjects (I already ran ?autorecon1
>> on them with no errors.) and I?m getting an error after the
>> ?final_surfs part saying that lh.white does not exits (and it doesn?t,
>> I checked for it).? I have run about 10 other subjects, and they all ran fine and contain ?h.white files.? I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
>> This error just started happening, and I didn?t change anything.? Here?s the command I?ve been using:
>>
>> ?
>>
>> recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
>> -autorecon2
>>
>> ?
>>
>> Here?s the error output:
>>
>> ?
>>
>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/an
>> alysis_files/ANG_1034/surf/lh.wh
>> ite): could not open file
>>
>> ?
>>
>> I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
>>
>> ?
>>
>> I?ve attached the recon-all.log file
>>
>> ?
>>
>> Thanks!
>>
>> ?
>>
>> ?
>>
>> ----
>>
>> ?
>>
>> Wade A. Weber, MS
>>
>> Psychiatry Research Program Coordinator
>>
>> ?
>>
>> Dell Medical School | The University of Texas at Austin
>>
>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>
>> ?
>>
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

------------------------------

Message: 2
Date: Fri, 22 Feb 2019 12:58:41 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [All] postdoctoral position in PET imaging
available at MGH / Martinos Center
To: freesurfer@nmr.mgh.harvard.edu
Cc: Marco Loggia <marco@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1902221258220.12350@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"




Postdoctoral position in integrated PET/MRI at Massachusetts General Hospital / Harvard Medical School

The Loggia and Hadjikhani Labs are inviting applications for a Post-Doctoral Research Fellow in the
Department of Radiology at Massachusetts General Hospital (A.A. Martinos Center for Biomedical Imaging)
and Harvard Medical School.

The candidate will use state-of-the-art integrated PET/MRI scanners to image neuroinflammation in the
central nervous systems of migraine patients, and the effect of nonpharmacological therapies. The
candidate will collaborate with Dr. Julie Price and several other members of the Martinos Center.

Requirements include a Ph.D. in Neuroscience, Physics, Chemistry, Engineering, or a related field, as
well as good command of written and oral English. Experience with Positron Emission Tomography is
preferred. Compensation is competitive and commensurate with experience.

If interested, please email Marco Loggia (marco@nmr.mgh.harvard.edu) with your CV.

?




_______________________________________________________

Marco L. Loggia, PhD
Assistant Professor of Radiology,?Harvard Medical School?
Associate Director, Center for Integrative?Pain NeuroImaging (CiPNI)

A. A. Martinos Center for Biomedical?Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-7267
Fax: (617) 726-7422?
Email: marco.loggia@mgh.harvard.edu
Web: http://scholar.harvard.edu/loggia





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------------------------------

Message: 3
Date: Fri, 22 Feb 2019 18:02:20 +0000
From: "Weber, Wade A" <wade.weber@austin.utexas.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR06MB53223C58673990E51A43EA42CA7F0@DM6PR06MB5322.namprd06.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

> External Email - Use Caution
>
> Hi Bruce,
>
> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.
>
> Wade
>
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:38 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> from the recon-all.log it looks like you never ran autorecon3. Is
> there a reason for this? Usually we run all the way through autorecon3
> before running the T2pial stuff
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>
>>
>> ????????External Email - Use Caution
>>
>> Hi all,
>>
>> ?
>>
>> I?m trying to run ?autorecon2 on 3 subjects (I already ran
>> ?autorecon1 on them with no errors.) and I?m getting an error after
>> the ?final_surfs part saying that lh.white does not exits (and it
>> doesn?t, I checked for it).? I have run about 10 other subjects, and they all ran fine and contain ?h.white files.? I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
>> This error just started happening, and I didn?t change anything.? Here?s the command I?ve been using:
>>
>> ?
>>
>> recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
>> -autorecon2
>>
>> ?
>>
>> Here?s the error output:
>>
>> ?
>>
>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
>> n
>> alysis_files/ANG_1034/surf/lh.wh
>> ite): could not open file
>>
>> ?
>>
>> I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
>>
>> ?
>>
>> I?ve attached the recon-all.log file
>>
>> ?
>>
>> Thanks!
>>
>> ?
>>
>> ?
>>
>> ----
>>
>> ?
>>
>> Wade A. Weber, MS
>>
>> Psychiatry Research Program Coordinator
>>
>> ?
>>
>> Dell Medical School | The University of Texas at Austin
>>
>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>
>> ?
>>
>>
>>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>



------------------------------

Message: 4
Date: Fri, 22 Feb 2019 18:04:23 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8b938318-34f9-a43e-5b73-a75ea4397797@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

what do you mean the surface is still messed up in freeview?

On 2/22/19 8:58 AM, Loucao, Ricardo wrote:

External Email - Use Caution

Thanks for the reply!
I tried the --vol-geom orig.mgz option but to no avail.

Small update: I inspected the metadata on the surface files using mris_info and discovered that the ctr property was different between the CAT generated surface and the pial surface that was produced from recon-all, while all the other transforms where the same.

So I figured the difference in the ctr should be compensated by a translation.

To do that, I first created a CAT2FS.fslmat transform of the form:

1 0 0 (CAT.ctr(1)-FS.ctr(1))
0 1 0 (CAT.ctr(3)-FS.ctr(3))
0 0 0 (CAT.ctr(2)-FS.ctr(2))
0 0 0 1

(NOTE: Im sure the order of the translation portion of the matrix has something to do with the orientation convention but I couldnt be bothered to dig deeper - I got this by trial and error)

and then converted it to LTA using lta_convert:

lta_convert --infsl CAT2FS.fslmat --outlta CAT2FS.lta --src orig.mgz --trg orig.mgz

and then applied this transformation using mris_transform:

mris_transform ?h.CAT CAT2FS.lta ?h.CATreg

sure enough when I load CATreg on tkregister2 I see everything perfectly aligned, but after doing mri_vol2surf the surface overlay is still messed up in Freeview. Any suggestions?

Thanks in advance for the help!

Ricardo



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Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
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Message: 5
Date: Fri, 22 Feb 2019 13:05:47 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1902221305410.12350@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

> External Email - Use Caution
>
> I can, but how will autorecon3 run without finishing autorecon2?
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:58 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.
>>
>> Wade
>>
>>
>> -----Original Message-----
>> From: freesurfer-bounces@nmr.mgh.harvard.edu
>> <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
>> Sent: Friday, February 22, 2019 11:38 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] ?h.white does not exist
>>
>> Hi Wade
>>
>> from the recon-all.log it looks like you never ran autorecon3. Is
>> there a reason for this? Usually we run all the way through autorecon3
>> before running the T2pial stuff
>>
>> cheers
>> Bruce
>> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>>
>>>
>>> ????????External Email - Use Caution
>>>
>>> Hi all,
>>>
>>> ?
>>>
>>> I?m trying to run ?autorecon2 on 3 subjects (I already ran
>>> ?autorecon1 on them with no errors.) and I?m getting an error after
>>> the ?final_surfs part saying that lh.white does not exits (and it
>>> doesn?t, I checked for it).? I have run about 10 other subjects, and they all ran fine and contain ?h.white files.? I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
>>> This error just started happening, and I didn?t change anything.? Here?s the command I?ve been using:
>>>
>>> ?
>>>
>>> recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
>>> -autorecon2
>>>
>>> ?
>>>
>>> Here?s the error output:
>>>
>>> ?
>>>
>>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
>>> n
>>> alysis_files/ANG_1034/surf/lh.wh
>>> ite): could not open file
>>>
>>> ?
>>>
>>> I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
>>>
>>> ?
>>>
>>> I?ve attached the recon-all.log file
>>>
>>> ?
>>>
>>> Thanks!
>>>
>>> ?
>>>
>>> ?
>>>
>>> ----
>>>
>>> ?
>>>
>>> Wade A. Weber, MS
>>>
>>> Psychiatry Research Program Coordinator
>>>
>>> ?
>>>
>>> Dell Medical School | The University of Texas at Austin
>>>
>>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>>
>>> ?
>>>
>>>
>>>
>>
>> _______________________________________________
>> 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
>
>
>

------------------------------

Message: 6
Date: Fri, 22 Feb 2019 18:07:42 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all -hires
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8b1e6a56-da29-dae2-d23f-6802320751fb@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

sometimes the -hires flag does not work very well. For the subjects where it does complete, do the surfaces look ok? You can also use recon-all.v6.hires with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for your reply.

Here is my command:

recon-all -all -s ${subj} -i ./${subj}/anat/016/mT1v2.nii -expert ./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna


________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu>
Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same issue with another
> subject before, and I had to terminate the recon-all and run it without -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
> cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
> cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
> mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
> mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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Message: 7
Date: Fri, 22 Feb 2019 18:11:14 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <73293c34-1dfd-af10-5c29-eef78dcd217d@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in the middle of autorecon3. If you don't spec autorecon3, then it will skip the initial part of autorecon3, and that is what is causing the error

On 2/22/19 1:05 PM, Bruce Fischl wrote:
no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A wrote:

External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.

Wade


-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:


External Email - Use Caution

Hi all,



I?m trying to run ?autorecon2 on 3 subjects (I already ran
?autorecon1 on them with no errors.) and I?m getting an error after
the ?final_surfs part saying that lh.white does not exits (and it
doesn?t, I checked for it). I have run about 10 other subjects, and they all ran fine and contain ?h.white files. I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
This error just started happening, and I didn?t change anything. Here?s the command I?ve been using:



recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
-autorecon2



Here?s the error output:



MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file



I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6



I?ve attached the recon-all.log file



Thanks!





----



Wade A. Weber, MS

Psychiatry Research Program Coordinator



Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu






_______________________________________________
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Message: 8
Date: Fri, 22 Feb 2019 18:11:17 +0000
From: "Weber, Wade A" <wade.weber@austin.utexas.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR06MB5322958EED752FACDBB80FB9CA7F0@DM6PR06MB5322.namprd06.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

But that's the problem. Autorecon2 won't finish because it's looking for lh.white, and it's not being made. I tried to run just "recon-all -white" to see if that would create it, and it still didn't.

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 12:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

> External Email - Use Caution
>
> I can, but how will autorecon3 run without finishing autorecon2?
>
> -----Original Message-----
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:58 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A
> wrote:
>
>> External Email - Use Caution
>>
>> Hi Bruce,
>>
>> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.
>>
>> Wade
>>
>>
>> -----Original Message-----
>> From: freesurfer-bounces@nmr.mgh.harvard.edu
>> <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
>> Sent: Friday, February 22, 2019 11:38 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] ?h.white does not exist
>>
>> Hi Wade
>>
>> from the recon-all.log it looks like you never ran autorecon3. Is
>> there a reason for this? Usually we run all the way through
>> autorecon3 before running the T2pial stuff
>>
>> cheers
>> Bruce
>> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>>
>>>
>>> ????????External Email - Use Caution
>>>
>>> Hi all,
>>>
>>> ?
>>>
>>> I?m trying to run ?autorecon2 on 3 subjects (I already ran
>>> ?autorecon1 on them with no errors.) and I?m getting an error after
>>> the ?final_surfs part saying that lh.white does not exits (and it
>>> doesn?t, I checked for it).? I have run about 10 other subjects, and they all ran fine and contain ?h.white files.? I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
>>> This error just started happening, and I didn?t change anything.? Here?s the command I?ve been using:
>>>
>>> ?
>>>
>>> recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
>>> -autorecon2
>>>
>>> ?
>>>
>>> Here?s the error output:
>>>
>>> ?
>>>
>>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/
>>> a
>>> n
>>> alysis_files/ANG_1034/surf/lh.wh
>>> ite): could not open file
>>>
>>> ?
>>>
>>> I?m running
>>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> on a virtual machine running Red Hat Enterprise Linux Workstation
>>> 7.6
>>>
>>> ?
>>>
>>> I?ve attached the recon-all.log file
>>>
>>> ?
>>>
>>> Thanks!
>>>
>>> ?
>>>
>>> ?
>>>
>>> ----
>>>
>>> ?
>>>
>>> Wade A. Weber, MS
>>>
>>> Psychiatry Research Program Coordinator
>>>
>>> ?
>>>
>>> Dell Medical School | The University of Texas at Austin
>>>
>>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>>
>>> ?
>>>
>>>
>>>
>>
>> _______________________________________________
>> 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
>
>
>



------------------------------

Message: 9
Date: Fri, 22 Feb 2019 18:15:25 +0000
From: "Weber, Wade A" <wade.weber@austin.utexas.edu>
Subject: Re: [Freesurfer] ?h.white does not exist
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR06MB532298C46F86DC5A55099AD1CA7F0@DM6PR06MB5322.namprd06.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Ahhhhhh. That makes sense, now. I will do that, then. Thank you!

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Friday, February 22, 2019 12:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ?h.white does not exist

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in the middle of autorecon3. If you don't spec autorecon3, then it will skip the initial part of autorecon3, and that is what is causing the error
On 2/22/19 1:05 PM, Bruce Fischl wrote:
no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A wrote:


External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:


External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.

Wade


-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:



External Email - Use Caution

Hi all,



I?m trying to run ?autorecon2 on 3 subjects (I already ran
?autorecon1 on them with no errors.) and I?m getting an error after
the ?final_surfs part saying that lh.white does not exits (and it
doesn?t, I checked for it). I have run about 10 other subjects, and they all ran fine and contain ?h.white files. I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
This error just started happening, and I didn?t change anything. Here?s the command I?ve been using:



recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial
-autorecon2



Here?s the error output:



MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file



I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6



I?ve attached the recon-all.log file



Thanks!





----



Wade A. Weber, MS

Psychiatry Research Program Coordinator



Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu





_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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Message: 10
Date: Fri, 22 Feb 2019 19:19:47 +0100
From: "Ey Dude" <Ey.Dude@gmx.net>
Subject: [Freesurfer] downsampling orig.mgz
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-7ce02207-f0a8-46a4-90fb-60a16de89379-1550859587886@3c-app-gmx-bs56>

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Message: 11
Date: Fri, 22 Feb 2019 18:29:20 +0000
From: "Nasiriavanaki, Zahra" <ZNASIRIAVANAKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all -hires
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<DM6PR04MB4443C261793F7954CA9BB20A997F0@DM6PR04MB4443.namprd04.prod.outlook.com>

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Hi Doug


Thank you very much for your reply.

Actually the recon finished today without any error. It just took so long to be done for only one subject (almost two days!)!

I checked the registration and It looks ok.

I will try -conf2hires for my other subject that -hires didn't work on it.


Thanks

Mona

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Friday, February 22, 2019 1:07:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -hires

sometimes the -hires flag does not work very well. For the subjects where it does complete, do the surfaces look ok? You can also use recon-all.v6.hires with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for your reply.

Here is my command:

recon-all -all -s ${subj} -i ./${subj}/anat/016/mT1v2.nii -expert ./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna


________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu>
Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same issue with another
> subject before, and I had to terminate the recon-all and run it without -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
> cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
> cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
> mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
> mris_fix_topology -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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Message: 12
Date: Fri, 22 Feb 2019 18:47:01 +0000
From: john Anderson <John.anderso@protonmail.com>
Subject: Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<g4ZSwMk7H0VaoNRunZqJOcncXIoPCdidhbqi4i8TwpeuPKpbgpiXlGkAtJP6G-47hz11LxlfNTJFadwbTe5OGUqbbpQG0UJHm_aESZdfYn0=@protonmail.com>

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi Dr Greve,

Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command fslmaths something like
fslmaths pet.nii -mask mask -inm 1 pet_normalized_whole_brain.nii.gz

For kinetic modeling.. kindly I would like to be sure that I got it right.
I am doing kinetic modeling for two groups of subjects patients and controls.
I am following PET surfer tutorial. In the case of patients and healthy controls comparison I can use MRTM1 and MRTM2 correct?

Also for the flag "--km-hb" are the IDs that I need to feed to this flag represent regions of high binding affinity in patients or healthy controls or it doesn't matter just regions known to have high binding. For example some tracers show regions of high binding affinity on healthy scans as well as patients scans.

On 2/22/19 11:43 AM, john Anderson wrote:

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological regions and the results were very confusing.... Based on your response bellow, I understand that for pathological regions I can feed "bp.nii.gz" files from "MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

You can actually use either MRTM1 or MRTM2 for further analysis, but I think the way I have it documented, you would use MRTM2.

Also for the flag "--km-ref", I have interest in doing whole brain normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let --km-ref know that I want to do whole brain normalization without feeding a very long list of numbers?

No, I don't think so. Sorry, I never considered this case. Are you sure that is what you want to do?

Thank you so much for help

John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is straightforward and easy to use. Thank you so much! I would appreciate any clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for normalizing PET signal. in the linear below the reference region is cerebellum cortex. If we need to normalize to occipital just we change the numbers based on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the regions that are pathologically involved where we expect it to have higher PET signal OR it represent the regions where PET tracer has the maximum binding in general regardless of pathology? I mean every tracer have high level in specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,

John

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Message: 13
Date: Fri, 22 Feb 2019 21:24:31 +0200
From: Francesca Strappini <francescastrappini@gmail.com>
Subject: Re: [Freesurfer] registration and resampling in native space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADHRBRp8yZYL9FzpuGDhiBRh0WJQ_7aQ7+ShNXqu2A-LaJUtnA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Thanks a lot, Doug!
I run the preprocessing:
preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
And the runs look well registered.

Then I run mri_label2vol:
mri_label2vol --seg
/home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
--reg register.dof6.lta --temp template.nii.gz --o
sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz

The region is in the correct space but completely misaligned. The
misalignment is even bigger than the unregistered region. Maybe I'm not
running the function correctly.
This set of regions are in the same space of the functional data but
registered to the raw T1.

Best
Francesca

Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> ha scritto:

> There should be a registration file called register.dof6.lta. Use that
> with mri_label2vol passing your segmentation in with --seg. Run with --help
> to get more info
>
> On 2/21/19 11:54 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thanks a lot!
> Running preproc-sess with the --per-session flag is exactly was I was
> looking for!
> Now that my functional runs are correctly registered to a reference image
> (so, to each other) I need to register them to a dataset of ROIs that were
> created outside freesurfer. These regions are in volume space and have the
> same resolution and box size of the functional runs. They are registered to
> the T1 that was used for the reconstruction of the surface. I've tried
> different functions for the registration but nothing really worked. I
> suppose I need a registration matrix that relates these regions to the
> reference image I used during the preprocessing and to apply this to each
> region. What's the best procedure?
>
> Best
> Francesca
>
>
> Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> ha scritto:
>
>> Yes, if you run it with the --targ as orig.mgz for the given subject,
>> then it will sample each run into the anatomical space (this can create
>> enourmous data data files!). Alternatively, you can run preproc-sess
>> with the --per-session flag and it will align all the runs to a single
>> template but otherwise keep everything in the functional space
>>
>> On 2/20/19 11:53 AM, Francesca Strappini wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I'll try to find some visual way to show what I mean, but it's really
>> > something mild and probably negligible.
>> > Do you know if is it possible with mri_vol2vol to give to all the runs
>> > that belong to the same subject the same system coordinates? So that
>> > each voxel across runs will have the same coordinates. I noticed that
>> > the transformation matrix is written in the header but it's not really
>> > applied to the data. Thank you!
>> >
>> >
>> > Best
>> > Francesca
>> >
>> >
>> > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Hi Francesca
>> >
>> > can you send us an image that shows why you think it can be
>> improved?
>> >
>> > cheers
>> > Bruce
>> > On
>> > Mon, 18 Feb 2019, Francesca Strappini wrote:
>> >
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Thank you!Now the registration is better but still not perfect.
>> > Is there a way to improve it?
>> > >
>> > > Best
>> > >
>> > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha
>> > > scritto:
>> > > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
>> > weighted? If so,
>> > > you should use --t2 instead of --t1 in bbregister
>> > >
>> > > On 2/14/19 2:18 PM, Francesca Strappini wrote:
>> > > >
>> > > > External Email - Use Caution
>> > > >
>> > > > Hi Doug,
>> > > >
>> > > > Could you advise me about how to correctly run
>> mri_vol2vol?
>> > > > The functional data did not get perfectly registered to
>> > the anatomy so
>> > > > I'm afraid I'm not running it correctly.
>> > > >
>> > > > Thanks!
>> > > >
>> > > >
>> > > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
>> > > > <fischl@nmr.mgh.harvard.edu
>> > <mailto:fischl@nmr.mgh.harvard.edu>
>> > <mailto:fischl@nmr.mgh.harvard.edu
>> > <mailto:fischl@nmr.mgh.harvard.edu>>> ha
>> > > > scritto:
>> > > >
>> > > > Hi Francesca
>> > > >
>> > > > sorry, I defer to Doug on the details of mri_vol2vol.
>> > > >
>> > > > cheers
>> > > > Bruce
>> > > >
>> > > > On Tue, 12 Feb 2019,
>> > > > Francesca Strappini wrote:
>> > > >
>> > > > >
>> > > > > External Email - Use Caution
>> > > > >
>> > > > > Thank you for the reply!
>> > > > > I run:
>> > > > > mri_vol2vol --reg register.dat --mov
>> > func_data.nii.gz --targ
>> > > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
>> > > > func_data_registered2T1.nii.gz --no-resample
>> > > > >
>> > > > > Then I checked the registration and it seems that
>> > the original
>> > > > run is better aligned to the T1 than
>> > > > > the registered one. Maybe am I not running
>> > mri_vol2vol correctly?
>> > > > >
>> > > > > Thanks!
>> > > > > Best
>> > > > >
>> > > > >
>> > > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce
>> Fischl
>> > > > <fischl@nmr.mgh.harvard.edu
>> > <mailto:fischl@nmr.mgh.harvard.edu>
>> > <mailto:fischl@nmr.mgh.harvard.edu
>> > <mailto:fischl@nmr.mgh.harvard.edu>>>
>> > > > ha scritto:
>> > > > > Hi Francesca
>> > > > >
>> > > > > check out the --no-resample option in
>> > mri_vol2vol. It just
>> > > > changes the
>> > > > > header, so I think should do what you want.
>> > > > >
>> > > > > cheers
>> > > > > Bruce
>> > > > >
>> > > > >
>> > > > > On Tue, 12 Feb 2019, Francesca Strappini
>> wrote:
>> > > > >
>> > > > > >
>> > > > > > External Email - Use Caution
>> > > > > >
>> > > > > > Dear Freesurfer's experts,
>> > > > > >
>> > > > > > I would like to register some functional
>> > data to the T1,
>> > > > that were collected in
>> > > > > separate days.
>> > > > > > I used bbregister:
>> > > > > >
>> > > > > > bbregister --s sub3 --mov func_data.nii.gz
>> > - --reg
>> > > > register.dat --init-coreg --t1
>> > > > > >
>> > > > > > Now, I would like to resample the data
>> > based on the
>> > > > register.dat without upsampling
>> > > > > and keeping the
>> > > > > > same FoV (3x3x3 mm; 64 64 50). Is it doable?
>> > > > > >
>> > > > > > Thanks!
>> > > > > > Best
>> > > > > >
>> > > > > >
>> > > > > > --
>> > > > > > Francesca Strappini, Ph.D.
>> > > > > > Neurobiology Department
>> > > > > > Weizmann Institute of Science
>> > > > > > 234 Herzl Street, Rehovot 7610001 Israel
>> > > > > > Tel.: +972 58 444 2584
>> > > > > > E-mail: francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>
>> > > > <mailto:francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>>
>> > > > > >
>> > > > > >_______________________________________________
>> > > > > Freesurfer mailing list
>> > > > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> > > > >
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Francesca Strappini, Ph.D.
>> > > > > Neurobiology Department
>> > > > > Weizmann Institute of Science
>> > > > > 234 Herzl Street, Rehovot 7610001 Israel
>> > > > > Tel.: +972 58 444 2584
>> > > > > E-mail: francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>
>> > > > <mailto:francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>>
>> > > > >
>> > > > >_______________________________________________
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Francesca Strappini, Ph.D.
>> > > > Neurobiology Department
>> > > > Weizmann Institute of Science
>> > > > 234 Herzl Street, Rehovot 7610001 Israel
>> > > > Tel.: +972 58 444 2584
>> > > > E-mail: francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>
>> > > > <mailto:francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>>
>> > > >
>> > > > _______________________________________________
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > >
>> > > _______________________________________________
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > >
>> > >
>> > > --
>> > > Francesca Strappini, Ph.D.
>> > > Neurobiology Department
>> > > Weizmann Institute of Science
>> > > 234 Herzl Street, Rehovot 7610001 Israel
>> > > Tel.: +972 58 444 2584
>> > > E-mail: francesca.strappini@weizmann.ac.il
>> > <mailto:francesca.strappini@weizmann.ac.il>
>> > >
>> > >_______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu <mailto:
>> 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
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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



--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il
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Message: 14
Date: Fri, 22 Feb 2019 20:15:31 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4a3f458c-e884-0881-51ec-b0485d07f85e@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"



On 2/22/19 1:47 PM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command fslmaths something like
fslmaths pet.nii -mask mask -inm 1 pet_normalized_whole_brain.nii.gz

For kinetic modeling.. kindly I would like to be sure that I got it right.
I am doing kinetic modeling for two groups of subjects patients and controls.
I am following PET surfer tutorial. In the case of patients and healthy controls comparison I can use MRTM1 and MRTM2 correct?
I don't know about DPA713. Generally, there will be a lot of studies done to verify the kinetic models that can be used. MRTM2 makes more assumptions than MRTM1, so it is not applicable to everything.

Also for the flag "--km-hb" are the IDs that I need to feed to this flag represent regions of high binding affinity in patients or healthy controls or it doesn't matter just regions known to have high binding. For example some tracers show regions of high binding affinity on healthy scans as well as patients scans.
Again, you should look through the literature and see what people have done to verify MRTM2 for your tracer.



On 2/22/19 11:43 AM, john Anderson wrote:

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological regions and the results were very confusing.... Based on your response bellow, I understand that for pathological regions I can feed "bp.nii.gz" files from "MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

You can actually use either MRTM1 or MRTM2 for further analysis, but I think the way I have it documented, you would use MRTM2.



Also for the flag "--km-ref", I have interest in doing whole brain normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let --km-ref know that I want to do whole brain normalization without feeding a very long list of numbers?

No, I don't think so. Sorry, I never considered this case. Are you sure that is what you want to do?



Thank you so much for help

John



On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is straightforward and easy to use. Thank you so much! I would appreciate any clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for normalizing PET signal. in the linear below the reference region is cerebellum cortex. If we need to normalize to occipital just we change the numbers based on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale


2) --km-hb define the high binding regions. Are these regions represent the regions that are pathologically involved where we expect it to have higher PET signal OR it represent the regions where PET tracer has the maximum binding in general regardless of pathology? I mean every tracer have high level in specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them for the HB region as their kinetics may be different than healthy tissue.



Thanks for any clarification,

John




_______________________________________________


Freesurfer mailing list


Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>


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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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Message: 15
Date: Fri, 22 Feb 2019 20:18:00 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] registration and resampling in native space
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3f243db7-63a9-a4e1-2b09-8a5c80190dec@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

That looks right. Can you verify that the seg (sourcedata...) is in the conformed anatomical space? Use mri_info can compare the output (particularly the vox2ras matrix) against orig.mgz. If they are the same, you can try adding --invertmtx to the mri_label2vol command line.

On 2/22/19 2:24 PM, Francesca Strappini wrote:

External Email - Use Caution

Thanks a lot, Doug!
I run the preprocessing:
preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
And the runs look well registered.

Then I run mri_label2vol:
mri_label2vol --seg /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz --reg register.dof6.lta --temp template.nii.gz --o sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz

The region is in the correct space but completely misaligned. The misalignment is even bigger than the unregistered region. Maybe I'm not running the function correctly.
This set of regions are in the same space of the functional data but registered to the raw T1.

Best
Francesca

Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> ha scritto:
There should be a registration file called register.dof6.lta. Use that with mri_label2vol passing your segmentation in with --seg. Run with --help to get more info

On 2/21/19 11:54 AM, Francesca Strappini wrote:

External Email - Use Caution

Thanks a lot!
Running preproc-sess with the --per-session flag is exactly was I was looking for!
Now that my functional runs are correctly registered to a reference image (so, to each other) I need to register them to a dataset of ROIs that were created outside freesurfer. These regions are in volume space and have the same resolution and box size of the functional runs. They are registered to the T1 that was used for the reconstruction of the surface. I've tried different functions for the registration but nothing really worked. I suppose I need a registration matrix that relates these regions to the reference image I used during the preprocessing and to apply this to each region. What's the best procedure?

Best
Francesca


Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> ha scritto:
Yes, if you run it with the --targ as orig.mgz for the given subject,
then it will sample each run into the anatomical space (this can create
enourmous data data files!). Alternatively, you can run preproc-sess
with the --per-session flag and it will align all the runs to a single
template but otherwise keep everything in the functional space

On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> I'll try to find some visual way to show what I mean, but it's really
> something mild and probably negligible.
> Do you know if is it possible with mri_vol2vol to give to all the runs
> that belong to the same subject the same system coordinates? So that
> each voxel across runs will have the same coordinates. I noticed that
> the transformation matrix is written in the header but it's not really
> applied to the data. Thank you!
>
>
> Best
> Francesca
>
>
> On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
> <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>> wrote:
>
> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> <DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>> ha
> > scritto:
> > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> weighted? If so,
> > you should use --t2 instead of --t1 in bbregister
> >
> > On 2/14/19 2:18 PM, Francesca Strappini wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Doug,
> > >
> > > Could you advise me about how to correctly run mri_vol2vol?
> > > The functional data did not get perfectly registered to
> the anatomy so
> > > I'm afraid I'm not running it correctly.
> > >
> > > Thanks!
> > >
> > >
> > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> > > <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>>> ha
> > > scritto:
> > >
> > > Hi Francesca
> > >
> > > sorry, I defer to Doug on the details of mri_vol2vol.
> > >
> > > cheers
> > > Bruce
> > >
> > > On Tue, 12 Feb 2019,
> > > Francesca Strappini wrote:
> > >
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Thank you for the reply!
> > > > I run:
> > > > mri_vol2vol --reg register.dat --mov
> func_data.nii.gz --targ
> > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> > > func_data_registered2T1.nii.gz --no-resample
> > > >
> > > > Then I checked the registration and it seems that
> the original
> > > run is better aligned to the T1 than
> > > > the registered one. Maybe am I not running
> mri_vol2vol correctly?
> > > >
> > > > Thanks!
> > > > Best
> > > >
> > > >
> > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> > > <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>>>
> > > ha scritto:
> > > > Hi Francesca
> > > >
> > > > check out the --no-resample option in
> mri_vol2vol. It just
> > > changes the
> > > > header, so I think should do what you want.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Tue, 12 Feb 2019, Francesca Strappini wrote:
> > > >
> > > > >
> > > > > External Email - Use Caution
> > > > >
> > > > > Dear Freesurfer's experts,
> > > > >
> > > > > I would like to register some functional
> data to the T1,
> > > that were collected in
> > > > separate days.
> > > > > I used bbregister:
> > > > >
> > > > > bbregister --s sub3 --mov func_data.nii.gz
> - --reg
> > > register.dat --init-coreg --t1
> > > > >
> > > > > Now, I would like to resample the data
> based on the
> > > register.dat without upsampling
> > > > and keeping the
> > > > > same FoV (3x3x3 mm; 64 64 50). Is it doable?
> > > > >
> > > > > Thanks!
> > > > > Best
> > > > >
> > > > >
> > > > > --
> > > > > Francesca Strappini, Ph.D.
> > > > > Neurobiology Department
> > > > > Weizmann Institute of Science
> > > > > 234 Herzl Street, Rehovot 7610001 Israel
> > > > > Tel.: +972 58 444 2584
> > > > > E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>
> > > <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>>
> > > > >
> > > > >_______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > >
> > > >
> > > > --
> > > > Francesca Strappini, Ph.D.
> > > > Neurobiology Department
> > > > Weizmann Institute of Science
> > > > 234 Herzl Street, Rehovot 7610001 Israel
> > > > Tel.: +972 58 444 2584
> > > > E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>
> > > <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>>
> > > >
> > > >_______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > > --
> > > Francesca Strappini, Ph.D.
> > > Neurobiology Department
> > > Weizmann Institute of Science
> > > 234 Herzl Street, Rehovot 7610001 Israel
> > > Tel.: +972 58 444 2584
> > > E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>
> > > <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
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> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>
> <mailto:francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>>
> >
> >_______________________________________________
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>



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--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il<mailto:francesca.strappini@weizmann.ac.il>



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Message: 16
Date: Fri, 22 Feb 2019 15:18:49 -0500
From: Haroon Popal <tuk12127@temple.edu>
Subject: [Freesurfer] vlrmerge for visualization only?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CANn27P=QgzkLzC6U7eETtzdzkrMsbgyUYFco+OyCa4a+mwOH1A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hello FreeSurfer Developers,

I have functional contrast maps from the HCP dataset. I converted these to
fsaverage space and now have GIFTIs for the surface data and a NIFTI for
the subcortical volume data. I would like to combine these into one file
for an analysis where I will be predicting the intensity of individual
voxels. I thought I would use vlrmerge to do this, but noticed that the
documentation notes that vlrmerge should only be used for
visualization purposes. I was wondering if you thought that doing my
analysis on the vlrmerge output would be a bad idea, even though I am not
doing any real computation on the merged volume maps.

If this is a bad idea, is there another method that I can use to combine
the surface and subcortical volume data?

Thank you.

--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University
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Message: 17
Date: Fri, 22 Feb 2019 20:18:48 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] downsampling orig.mgz
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c91b568f-2bba-7738-31fe-7b462e8759fc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

You do not need to downsample the orig.mgz in this case

On 2/22/19 1:19 PM, Ey Dude wrote:

External Email - Use Caution

Hi all,

I would like to downsample my fsnative mesh by a factor of 0.1 and sample my BOLD data to surface space in a next step. I have successfully downsampled my surf files using mris_decimate and mri_surf2surf. However, I am still not able to run mri_vol2surf as it is asking for the orig.mgz file which is not downsampled yet and which I do not know how to downsample. Do I have to use mri_convert to do so? Would I have to set 0.1 0.1 0.1 as my downsamling factor?

Thank you so much for your help!
Ella



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Message: 18
Date: Fri, 22 Feb 2019 20:24:14 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] vlrmerge for visualization only?
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <63a30c32-9378-dc36-8d5b-ff137e5c45f1@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

It depends on what you eventually want to do with it. The warning was so that people would not go off and do, eg, correction for multiple comparisons or something where there was some assumption about consistency between the surface-based and volume-based results.

On 2/22/19 3:18 PM, Haroon Popal wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I have functional contrast maps from the HCP dataset. I converted these to fsaverage space and now have GIFTIs for the surface data and a NIFTI for the subcortical volume data. I would like to combine these into one file for an analysis where I will be predicting the intensity of individual voxels. I thought I would use vlrmerge to do this, but noticed that the documentation notes that vlrmerge should only be used for visualization purposes. I was wondering if you thought that doing my analysis on the vlrmerge output would be a bad idea, even though I am not doing any real computation on the merged volume maps.

If this is a bad idea, is there another method that I can use to combine the surface and subcortical volume data?

Thank you.

--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University



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Message: 19
Date: Fri, 22 Feb 2019 15:42:08 -0500
From: Zhi Li <lizhi.psych@gmail.com>
Subject: [Freesurfer] Different paradigm files
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGnBb2MFXurLCy73THx2dB6-x8t9XO9E4X-SZaqGqbXzzinrrQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hello FreeSurfer experts,

It seems that all the subjects adopt a single same paradigm file in FsFast,
am I correct? So how to handle it if each subject has different paradigm
files, e.g., different onset time and duration? I could do the first-level
analysis in each individual data, however, I cannot concatenate data with
'isxconcat-sess' due to that there is not an analysis folder generated from
a same paradigm file. Any suggestions?

Thanks and best regards,

Lizhi
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Message: 20
Date: Fri, 22 Feb 2019 22:43:19 +0200
From: Francesca Strappini <francescastrappini@gmail.com>
Subject: Re: [Freesurfer] registration and resampling in native space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADHRBRoGT9o6g0qDYhoT9=ot53aPWVmZP-jyab3on4Jb_8=qKQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Thanks!
The vox2ras matrices are not same.

This is one region:

francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info
sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
type: nii
dimensions: 64 x 64 x 50
voxel sizes: 3.000000, 3.000000, 3.000000
type: FLOAT (3)
fov: 192.000
dof: 0
xstart: -96.0, xend: 96.0
ystart: -96.0, yend: 96.0
zstart: -75.0, zend: 75.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.9988, y_r = 0.0235, z_r = 0.0427, c_r =
-2.2923
: x_a = 0.0124, y_a = 0.9702, z_a = -0.2420, c_a =
19.4768
: x_s = 0.0471, y_s = 0.2412, z_s = 0.9693, c_s =
25.1269
Orientation : LAS
Primary Slice Direction: axial

voxel to ras transform:
-2.9964 0.0704 0.1281 88.1380
0.0373 2.9106 -0.7261 -56.7017
0.1414 0.7237 2.9080 -75.2534
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -27

ras to voxel transform:
-0.3329 0.0041 0.0157 30.7614
0.0078 0.3234 0.0804 23.6988
0.0142 -0.0807 0.3231 18.4853
-0.0000 -0.0000 -0.0000 1.0000

Orig:

francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info
orig.mgz
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
-2.3092
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
26.4827
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
19.0338

talairach xfm :
/usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal

voxel to ras transform:
-1.0000 0.0000 0.0000 125.6908
0.0000 0.0000 1.0000 -101.5173
0.0000 -1.0000 0.0000 147.0338
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform:
-1.0000 0.0000 0.0000 125.6908
-0.0000 0.0000 -1.0000 147.0338
-0.0000 1.0000 0.0000 101.5173
-0.0000 -0.0000 -0.0000 1.0000

This is the raw T1 to which the regions are registered:

Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz
type: nii
dimensions: 256 x 256 x 192
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -96.0, zend: 96.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.0069, y_r = -0.0360, z_r = -0.9993, c_r =
-2.3092
: x_a = -0.9823, y_a = 0.1874, z_a = -0.0000, c_a =
26.4827
: x_s = -0.1873, y_s = -0.9816, z_s = 0.0366, c_s =
19.0338
Orientation : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
-0.0069 -0.0360 -0.9993 99.1125
-0.9823 0.1874 -0.0000 128.2306
-0.1873 -0.9816 0.0366 165.1330
0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform:
-0.0069 -0.9823 -0.1873 157.5619
-0.0360 0.1874 -0.9816 141.6386
-0.9993 0.0000 0.0366 92.9949
-0.0000 -0.0000 -0.0000 1.0000



Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> ha scritto:

> That looks right. Can you verify that the seg (sourcedata...) is in the
> conformed anatomical space? Use mri_info can compare the output
> (particularly the vox2ras matrix) against orig.mgz. If they are the same,
> you can try adding --invertmtx to the mri_label2vol command line.
>
> On 2/22/19 2:24 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thanks a lot, Doug!
> I run the preprocessing:
> preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
> And the runs look well registered.
>
> Then I run mri_label2vol:
> mri_label2vol --seg
> /home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
> --reg register.dof6.lta --temp template.nii.gz --o
> sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz
>
> The region is in the correct space but completely misaligned. The
> misalignment is even bigger than the unregistered region. Maybe I'm not
> running the function correctly.
> This set of regions are in the same space of the functional data but
> registered to the raw T1.
>
> Best
> Francesca
>
> Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <
> DGREVE@mgh.harvard.edu> ha scritto:
>
>> There should be a registration file called register.dof6.lta. Use that
>> with mri_label2vol passing your segmentation in with --seg. Run with --help
>> to get more info
>>
>> On 2/21/19 11:54 AM, Francesca Strappini wrote:
>>
>> External Email - Use Caution
>> Thanks a lot!
>> Running preproc-sess with the --per-session flag is exactly was I was
>> looking for!
>> Now that my functional runs are correctly registered to a reference image
>> (so, to each other) I need to register them to a dataset of ROIs that were
>> created outside freesurfer. These regions are in volume space and have the
>> same resolution and box size of the functional runs. They are registered to
>> the T1 that was used for the reconstruction of the surface. I've tried
>> different functions for the registration but nothing really worked. I
>> suppose I need a registration matrix that relates these regions to the
>> reference image I used during the preprocessing and to apply this to each
>> region. What's the best procedure?
>>
>> Best
>> Francesca
>>
>>
>> Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <
>> DGREVE@mgh.harvard.edu> ha scritto:
>>
>>> Yes, if you run it with the --targ as orig.mgz for the given subject,
>>> then it will sample each run into the anatomical space (this can create
>>> enourmous data data files!). Alternatively, you can run preproc-sess
>>> with the --per-session flag and it will align all the runs to a single
>>> template but otherwise keep everything in the functional space
>>>
>>> On 2/20/19 11:53 AM, Francesca Strappini wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > I'll try to find some visual way to show what I mean, but it's really
>>> > something mild and probably negligible.
>>> > Do you know if is it possible with mri_vol2vol to give to all the runs
>>> > that belong to the same subject the same system coordinates? So that
>>> > each voxel across runs will have the same coordinates. I noticed that
>>> > the transformation matrix is written in the header but it's not really
>>> > applied to the data. Thank you!
>>> >
>>> >
>>> > Best
>>> > Francesca
>>> >
>>> >
>>> > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
>>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
>>> wrote:
>>> >
>>> > Hi Francesca
>>> >
>>> > can you send us an image that shows why you think it can be
>>> improved?
>>> >
>>> > cheers
>>> > Bruce
>>> > On
>>> > Mon, 18 Feb 2019, Francesca Strappini wrote:
>>> >
>>> > >
>>> > > External Email - Use Caution
>>> > >
>>> > > Thank you!Now the registration is better but still not perfect.
>>> > Is there a way to improve it?
>>> > >
>>> > > Best
>>> > >
>>> > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
>>> > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> ha
>>> > > scritto:
>>> > > Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
>>> > weighted? If so,
>>> > > you should use --t2 instead of --t1 in bbregister
>>> > >
>>> > > On 2/14/19 2:18 PM, Francesca Strappini wrote:
>>> > > >
>>> > > > External Email - Use Caution
>>> > > >
>>> > > > Hi Doug,
>>> > > >
>>> > > > Could you advise me about how to correctly run
>>> mri_vol2vol?
>>> > > > The functional data did not get perfectly registered to
>>> > the anatomy so
>>> > > > I'm afraid I'm not running it correctly.
>>> > > >
>>> > > > Thanks!
>>> > > >
>>> > > >
>>> > > > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
>>> > > > <fischl@nmr.mgh.harvard.edu
>>> > <mailto:fischl@nmr.mgh.harvard.edu>
>>> > <mailto:fischl@nmr.mgh.harvard.edu
>>> > <mailto:fischl@nmr.mgh.harvard.edu>>> ha
>>> > > > scritto:
>>> > > >
>>> > > > Hi Francesca
>>> > > >
>>> > > > sorry, I defer to Doug on the details of mri_vol2vol.
>>> > > >
>>> > > > cheers
>>> > > > Bruce
>>> > > >
>>> > > > On Tue, 12 Feb 2019,
>>> > > > Francesca Strappini wrote:
>>> > > >
>>> > > > >
>>> > > > > External Email - Use Caution
>>> > > > >
>>> > > > > Thank you for the reply!
>>> > > > > I run:
>>> > > > > mri_vol2vol --reg register.dat --mov
>>> > func_data.nii.gz --targ
>>> > > > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
>>> > > > func_data_registered2T1.nii.gz --no-resample
>>> > > > >
>>> > > > > Then I checked the registration and it seems that
>>> > the original
>>> > > > run is better aligned to the T1 than
>>> > > > > the registered one. Maybe am I not running
>>> > mri_vol2vol correctly?
>>> > > > >
>>> > > > > Thanks!
>>> > > > > Best
>>> > > > >
>>> > > > >
>>> > > > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce
>>> Fischl
>>> > > > <fischl@nmr.mgh.harvard.edu
>>> > <mailto:fischl@nmr.mgh.harvard.edu>
>>> > <mailto:fischl@nmr.mgh.harvard.edu
>>> > <mailto:fischl@nmr.mgh.harvard.edu>>>
>>> > > > ha scritto:
>>> > > > > Hi Francesca
>>> > > > >
>>> > > > > check out the --no-resample option in
>>> > mri_vol2vol. It just
>>> > > > changes the
>>> > > > > header, so I think should do what you want.
>>> > > > >
>>> > > > > cheers
>>> > > > > Bruce
>>> > > > >
>>> > > > >
>>> > > > > On Tue, 12 Feb 2019, Francesca Strappini
>>> wrote:
>>> > > > >
>>> > > > > >
>>> > > > > > External Email - Use Caution
>>> > > > > >
>>> > > > > > Dear Freesurfer's experts,
>>> > > > > >
>>> > > > > > I would like to register some functional
>>> > data to the T1,
>>> > > > that were collected in
>>> > > > > separate days.
>>> > > > > > I used bbregister:
>>> > > > > >
>>> > > > > > bbregister --s sub3 --mov func_data.nii.gz
>>> > - --reg
>>> > > > register.dat --init-coreg --t1
>>> > > > > >
>>> > > > > > Now, I would like to resample the data
>>> > based on the
>>> > > > register.dat without upsampling
>>> > > > > and keeping the
>>> > > > > > same FoV (3x3x3 mm; 64 64 50). Is it
>>> doable?
>>> > > > > >
>>> > > > > > Thanks!
>>> > > > > > Best
>>> > > > > >
>>> > > > > >
>>> > > > > > --
>>> > > > > > Francesca Strappini, Ph.D.
>>> > > > > > Neurobiology Department
>>> > > > > > Weizmann Institute of Science
>>> > > > > > 234 Herzl Street, Rehovot 7610001 Israel
>>> > > > > > Tel.: +972 58 444 2584
>>> > > > > > E-mail: francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>
>>> > > > <mailto:francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>>
>>> > > > > >
>>> > > > > >_______________________________________________
>>> > > > > Freesurfer mailing list
>>> > > > > Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > > > >
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > > > >
>>> > > > >
>>> > > > >
>>> > > > > --
>>> > > > > Francesca Strappini, Ph.D.
>>> > > > > Neurobiology Department
>>> > > > > Weizmann Institute of Science
>>> > > > > 234 Herzl Street, Rehovot 7610001 Israel
>>> > > > > Tel.: +972 58 444 2584
>>> > > > > E-mail: francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>
>>> > > > <mailto:francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>>
>>> > > > >
>>> > > > >_______________________________________________
>>> > > > Freesurfer mailing list
>>> > > > Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>>> > > >
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > > >
>>> > > >
>>> > > >
>>> > > > --
>>> > > > Francesca Strappini, Ph.D.
>>> > > > Neurobiology Department
>>> > > > Weizmann Institute of Science
>>> > > > 234 Herzl Street, Rehovot 7610001 Israel
>>> > > > Tel.: +972 58 444 2584
>>> > > > E-mail: francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>
>>> > > > <mailto:francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>>
>>> > > >
>>> > > > _______________________________________________
>>> > > > Freesurfer mailing list
>>> > > > Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > > >
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > >
>>> > >
>>> > > _______________________________________________
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > Francesca Strappini, Ph.D.
>>> > > Neurobiology Department
>>> > > Weizmann Institute of Science
>>> > > 234 Herzl Street, Rehovot 7610001 Israel
>>> > > Tel.: +972 58 444 2584
>>> > > E-mail: francesca.strappini@weizmann.ac.il
>>> > <mailto:francesca.strappini@weizmann.ac.il>
>>> > >
>>> > >_______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu <mailto:
>>> Freesurfer@nmr.mgh.harvard.edu>
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>>> >
>>> >
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>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> Francesca Strappini, Ph.D.
>> Neurobiology Department
>> Weizmann Institute of Science
>> 234 Herzl Street, Rehovot 7610001 Israel
>> Tel.: +972 58 444 2584
>> E-mail: francesca.strappini@weizmann.ac.il
>>
>> _______________________________________________
>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
>
>
>
> --
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strappini@weizmann.ac.il
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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



--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il
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Message: 21
Date: Fri, 22 Feb 2019 21:33:57 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Different paradigm files
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0c4e7038-af98-a2c8-715d-93e747e36656@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

While the name of the paradigm file must be the same across runs and subjects, the contents paradigm file can be different. That should be able to handle what you are doing

On 2/22/19 3:42 PM, Zhi Li wrote:

External Email - Use Caution

Hello FreeSurfer experts,

It seems that all the subjects adopt a single same paradigm file in FsFast, am I correct? So how to handle it if each subject has different paradigm files, e.g., different onset time and duration? I could do the first-level analysis in each individual data, however, I cannot concatenate data with 'isxconcat-sess' due to that there is not an analysis folder generated from a same paradigm file. Any suggestions?

Thanks and best regards,

Lizhi



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End of Freesurfer Digest, Vol 180, Issue 48
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