Re: [Freesurfer] Applying Pial edits to Longitudinal

[Martin Reuter]

Hi Sierra, 

the long command should be

recon-all -long C002d C002.base -mprage …..

same way as you called it the first time when using the -all flag.

Best, Martin



> On 8. Jun 2019, at 20:28, Sierra Ann Jarvis  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello Freesurfers, 
> 
> I am trying to apply Pial edits to my longitudinal time point. I have tried 
> the command,
> 
> recon-all -long C002d.long.C002.base/ C002.base -mprage -3T -norm2-b 20 
> -norm2-n 5 -autorecon2 -autorecon3
> 
> But receive the error, 
> 
> Unmatched “.
> 
> I am using  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> 
> Do you know what could be the reason for this?
> Sierra 
> ___
> 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

Re: [Freesurfer] Advantage of having skull for longitudinal processing?

[Martin Reuter]

Hi Adam, 

the longitudinal registration should not care, but the regular stream would 
like to have the skull in the image. This will help for a couple steps (full 
head talairach registration -> eTIV etc). 

Best, Martin


> On 5. Jun 2019, at 03:57, Adam Martersteck  wrote:
> 
> External Email - Use Caution
> 
> 
> Hi Freesurfer team,
> 
> I'm thinking of pre-skullstrip'ing my brains prior to being input into 
> FreeSurfer.
> 
> My fear was this information in the skull might be useful during 
> mri_robust_register or mri_robust_template for longitudinal analyses:
> 
> Martin discusses this in his Freesurfer workshop talk at 9 minutes in 
> (youtube: http://www.youtube.com/watch?v=vxJODPBLd3M&t=9m21s 
> ) where the heatmap 
> covers parts of the skull and the Freesurfer wiki which mentions that the 
> Tukey biweight will deweight regions of noise like tongue/eye/neck 
> differences.
> 
> But it appears the longitudinal stream registers everything on each 
> cross-sectional's norm.mgz to create the fused norm -- which is skullstripped 
> and missing neck/tongue/eyes/skull already.
> 
> Am I missing something? Is it alright if my T1.mgz, rawavg.mgz, orig.mgz, 
> etc. do not have a skull for longitudinal processing?
> 
> Thanks,
> Adam 
> ___
> 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

Re: [Freesurfer] Within-subject vertexwise correlation

[Matthieu Vanhoutte]

External Email - Use Caution

I effectively smoothed both modalities the same amount.

The question is whether I should or not smooth before calculating
within-subject correlation?

Best,
Matthieu

Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> I'm not sure that this is a question we can answer. If you do smooth, then
> you should smooth both modalities the same amount.
>
> On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> I would like to compute within-subject correlation between two modalities
> based on vertexwise maps in fsaverage space. I wonder whether I have to
> smooth the normalized surface-based maps before computing vertexwise
> within-subject correlation?
>
> I have noted that smoothing surface maps before computing correlation
> increases the output correlation value.
>
> Thanks for your lights.
>
> Best,
> Matthieu
>
> ___
> Freesurfer mailing 
> listfreesur...@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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] 4dfp data format

[Greve, Douglas N.,Ph.D.]

I don't know. I'm cc'ing Avi.

On 6/8/2019 1:04 AM, Francesca Pentimalli wrote:

External Email - Use Caution

Dear freesurfer experts,

I am trying to use the 4dfp data format, but I am not able to find the 4dfp 
suite of tools developed by Dr. Avi Snyder. Can someone please point me in the 
right direction?

Regards,
Francesca
--
Francesca Pentimalli Biscaretti di Ruffia
Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.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

Re: [Freesurfer] translations and rotations from an affine transform matrix

[Greve, Douglas N.,Ph.D.]

you can also use lta_convert to convert a .dat file to an LTA

On 6/22/2019 2:12 AM, Greve, Douglas N.,Ph.D. wrote:
If it is an LTA (not .dat file), you can use
mri_coreg --mat2par ltafile
There will be 9 values that come out:
1-3: translation in mm
4-6: rotation in deg
7-9: should all be 1s in this case

On 6/20/2019 2:52 AM, Pfannmoeller, Joerg Peter wrote:
Hello,

is there a tool to extract the translations and rotations from an affine 
transform matrix (register.dof6.dat)?

Best Joerg



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Confirmation regarding running GLM on command line stream

[Greve, Douglas N.,Ph.D.]

Hi, sorry for the delay.

On 6/7/2019 3:33 AM, Avi Gharehgazlou wrote:

External Email - Use Caution
Hi experts,

Will you please confirm below command lines I run to examine between group 
differences in LGI? I have 3 questions listed.

I can’t run the below line, it gives an error:
mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in lh.pial_lgi.fwhm0.fsaverage 
--target fsaverage --hemi lh --meas pial_lgi --out lh.pial_lgi.0.mgh
mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in rh.pial_lgi.fwhm0.fsaverage 
--target fsaverage --hemi rh --meas pial_lgi --out rh.pial_lgi.0.mgh

Therefore, I run the below line instead - although I know it’s for uncached 
data and I have already ran qcache for my subjects (using: recon-all -s 
101031_01 -qcache -measure pial_lgi)

mris_preproc --fsgd ASDvsADHD.txt --target fsaverage --hemi lh --meas pial_lgi 
--out lh.pial_lgi.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.pial_lgi.mgh --fwhm 0 --cortex 
--tval lh.pial_lgi.0.mgh
# I run above line separately for right hemisphere

1.   Do I have to write “cortex” in above command line or not?

No, not with --fwhm 0. In fact, you should not need to run that command at all.

2.   Is it okay to run this command line considering that qcache has 
already been run on all my subjects?

Yes

3.   I’ve ran qcache (and above command line) multiple times on each 
subject in my data. Is this ok? Or does this mess up anything?

No, it is fine.
To test for main effect of group, I ran below line:
mri_glmfit --y lh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C 
betweengroupdifferencecontrollingforageSAsex.mtx --C 
agebydiagnosisinteraction.mtx --surf fsaverage lh --cortex --glmdir 
lh.ASDvsADHD.glmdir
mri_glmfit --y rh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C 
betweengroupdifferencecontrollingforageSAsex.mtx --C 
agebydiagnosisinteraction.mtx --surf fsaverage rh --cortex --glmdir 
rh.ASDvsADHD.glmdir

To correct for multiple comparisons using monte carlo:
mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces
mri_glmfit-sim --glmdir rh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces
Those commands are technically fine, but you should not use a threshold of 1.3 
with MC correction as the false positive rates will be highly elevated. If you 
want to use 1.3, then you should use a permutation test. Otherwise, you should 
use at least 3.0

I'd really appreciate your soon reply,

Thanks so much for all your support,

Avi



___
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

Re: [Freesurfer] examining between group differences using DODS

[Greve, Douglas N.,Ph.D.]

On 6/7/2019 2:29 AM, Avi Gharehgazlou wrote:

External Email - Use Caution

Hi experts,

I want to examine between-group differences in LGI controlling for age, sex and 
surface area (all except sex demeaned).
To do so, I ran the DODS model on QDEC selecting:

- “diagnosis” and “sex” as discrete (fixed factors)

- “age” and “surface area” as nuisance factors

- And selected this question --> “Does the average pial_lgi, accounting 
for sex, differ between TD and NDD? Nuissance factors: Age Surface area”
1) I wanted to ask you what the significant results from the above analysis 
means?
I was under the impression that the significant clusters represent clusters 
where there are significant group differences in LGI while controlling for age, 
surface area and sex.
Correct.
But I am confused because I know from previous threads that you recommend to 
run DODS to check for interactions first, and if there is no interaction to 
then run DOSS to see differences between groups. So:
2) Do my significant results mean that I have an interaction between diagnosis 
and sex OR diagnosis and age OR diagnosis and surface area?
No, not from that contrast. QDEC might put out another contrasts that test for 
that. Otherwise, you will have to use the command line stream.
3) Considering that I have an interaction, how do I now examine between-group 
differences in LGI? Is what I have done (through the DODS model) correct?
If there is an interaction, then interpreting the results becomes more 
complicated as the size and direction then become dependent on the age and 
surface area. Test for the interaction and hope that there is none:).

I'd really appreciate your help,

Thanks so much,

Avi



___
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

Re: [Freesurfer] eTIV and brainmask mismatch on Philips data

[Greve, Douglas N.,Ph.D.]

If the registration looks ok then it probably means that the skull stripping 
was too aggressive. Have you looked at the skull stripping?

On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote:

External Email - Use Caution

Hi all!

We are running FS v.6.0. on a supercomputer operating on Linux. We have two 
sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. 
The T1 images on both scanners have comparable CNR, with an isotropic 
resolution of 1mm3 each. The recon-all finished with no errors, but in 
approximately half of the Philips data there is a significant (up to 40%) 
difference between the brain mask volume and eTIV (no such problem on Siemens). 
We inspected the Talairach registration (as is pointed that eTIV is calculated 
upon it) in the mismatched data with:

tkregister2 --mgz --s  --fstal --surf orig

and in the corrupted data the brain mask and the WM-GM borders align in terms 
of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" 
difference).

What may be the reason and how to cope with that? We cannot normalize the 
volume data to eTIV (as it is not proper), what value should we use instead?

Attached you will find example tkregister2 output screenshots.

Best regards,
Agnieszka Sabisz






___
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

Re: [Freesurfer] registration with bbr and determination of motion regressors with mcdat2mcextreg

[Greve, Douglas N.,Ph.D.]

That is fine. I don't think that there are any conventions you need to follow 
(it should just be an Nx6 matrix

On 6/13/2019 8:45 PM, Pfannmoeller, Joerg Peter wrote:
Hello,

I have used bbr to register all EPI volumes in my time series to the brains of 
my participants. The fMRI time series at each vertex was determined based on 
this registration. I would like to use motion regressors in the GLM analysis. 
Is it appropriate to extract the motion parameters from the bbr registration 
matrices to use them as input to mcdat2mcextreg? Are there any conventions I 
need to take into account?

Best Joerg



___
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

Re: [Freesurfer] hippocampal subfield as CONN seeds

[Greve, Douglas N.,Ph.D.]

There are several things that will need to be done, and they can be quite 
tricky. Since you already have a registration between the fMRI and the MNI, you 
will have to create a rigid registration from the FS anatomical to the fMRI, 
then concatenate the registrations into a single registration. You can then 
apply the registration to the  FS segementation with mri_label2vol using the 
--seg option. It will not be easy to extract all these matrices, sorry, I don't 
know enough about SPM to help  you out much more.

On 6/13/2019 5:37 PM, Nelson, Eric A wrote:

External Email - Use Caution
Thanks for your response,

I believe CONN should be using SPM linear?

Best,

Eric
From: Greve, Douglas N.,Ph.D. [mailto:dgr...@mgh.harvard.edu]
Sent: Wednesday, June 12, 2019 8:27 AM
To: Nelson, Eric A 
Subject: Re: [Freesurfer] hippocampal subfield as CONN seeds

I meant how does CONN do the registration? SPM linear? FSL non-linear? That 
command definitely will not work. You have to do it in exactly the same way as 
CONN or else the segmentations won't align.


On 6/12/2019 2:39 PM, Nelson, Eric A wrote:

External Email - Use Caution
Hi,

Not sure I sent this correctly the last time. Im not sure I understand the 
question because I have not successfully registered the hippoSfLabels file to 
mni space. I can load the hippoSfLabels.mgz file into CONN at the subject 
level, but I have two problems. 1st it is not in MNI space. 2nd it is the whole 
hippocampus and I want to be able to use masks of the individual subfields. To 
try and convert the hippoSfLabels file to MNI space though I used the following.

mri_vol2vol --mov lh.hippoSfLabels-T1-T2.v10.mgz \
--targ $FREESURFER_HOME/average/mni305.cor.mgz \
--xfm transforms/talairach.xfm  \
--o test.mgz

Eric


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception

[Greve, Douglas N.,Ph.D.]

tksurfer has some instabilities in it. It is obsolete and no longer being 
supported. Have you tried freeview? You can use tksurferfv which runs freeview 
with tksurfer options.

On 6/12/2019 6:54 PM, Wafaa Sweidan wrote:

External Email - Use Caution

Hello all,

I have been using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on macos high 
sierra, then I updated to mojave 10.14. freeusrfer was working all good for a 
while. BUT, for unknown reasons, I am no longer able to overlay the 
significance maps using tksurfer and cant open qdec, like below:

command: tksurfer fsaverage lh inflated

output error:
subject is fsaverage
hemiis lh
surface is inflated
surfer: current subjects dir: /Users/wsweidan/Desktop/GLM_trial
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/wsweidan/Desktop/GLM_trial
checking for nofix files in 'inflated'
Reading image info (/Users/wsweidan/Desktop/GLM_trial/fsaverage)
Reading /Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz
surfer: Reading header info from 
/Users/wsweidan/Desktop/GLM_trial/fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
setting percentile thresholds (-1.00, 0.00, 0.00)
surfer: using interface /Applications/freesurfer/tktools/tksurfer.tcl
Reading /Applications/freesurfer/tktools/tkm_common.tcl
Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl
Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /Applications/freesurfer/tktools/tkUtils.tcl
Error sourcing /Applications/freesurfer/tktools/tksurfer.tcl:
bad distance "0.125i": can't be negative
reading white matter vertex locations...
% Floating exception

command: qdec
output error: Floating exception

I reinstalled freesurfer again and I still get the same errors. Freeview works 
just fine. Any input of how to solve this issue?

Thanks in advance,
Wafaa




___
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

Re: [Freesurfer] bbregister- switched coronal and axial views error

[Greve, Douglas N.,Ph.D.]

What version of FS are you using? If before 6.0 (eg, 5,3), then it may 
be an error with the initialization. This is much improved in version 6.

On 6/18/2019 5:38 PM, Wenzhen Zhao wrote:
>  External Email - Use Caution
>
> Dear list,
>
> After running preproc-sess on fmri data, bbr-sum was 0.94. After looking 
> through images of template.nii.gz with register.dof6.lta file, I found that 
> coronal and axial views of template(w/ registration applied) are switched.
>
> $preproc-sess -s sess01 -fsd rest -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run
>
> Is there any possible error that I might have made?
> or is there any way to fix it?
>
> I appreciate your help!
>
> Thanks,
> Wenzhen
>
> ___
> 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

Re: [Freesurfer] Within-subject vertexwise correlation

[Greve, Douglas N.,Ph.D.]

I'm not sure that this is a question we can answer. If you do smooth, then you 
should smooth both modalities the same amount.

On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear FS experts,

I would like to compute within-subject correlation between two modalities based 
on vertexwise maps in fsaverage space. I wonder whether I have to smooth the 
normalized surface-based maps before computing vertexwise within-subject 
correlation?

I have noted that smoothing surface maps before computing correlation increases 
the output correlation value.

Thanks for your lights.

Best,
Matthieu



___
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

Re: [Freesurfer] Fwd: freesurfer picture

[Greve, Douglas N.,Ph.D.]

You will have to find the qdec output folder. There will be a subfolder for 
each contrast. Load the sig.mgh file in the contrast subfolder, eg,
tksurferfv fsaverage lh inflated -aparc -overalay sig.mgh
tksurferfv is just a convenient front end for freeview (fv)


On 6/17/2019 1:56 PM, Abby tang wrote:

External Email - Use Caution

Hi Bruce
I want to compare the relationship between age and thickness, which is 
controlled the effect about sex,education and eTIV. I want to get more 
beautiful pictures, but the ability of QDEC is limited.
I have tried freeview, but I don't know what file should be loaded in freeview. 
 After qdec processing, what file format should be selected to load freeview? 
Or if there are other method to use frreview direct to regressive age and 
thickness?
Could you give me some advices?
Thank you! Hope your reply.
best wish
Abby

Abby tang mailto:abbytang0...@gmail.com>> 于2019年6月5日周三 
下午10:32写道：
Hi Bruce
I have tried freeview, but I don't know what file should be loaded in freeview. 
 After qdec processing, what file format should be selected to load freeview?
best wish
Abby

Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> 
于2019年6月5日周三 下午9:53写道：
Hi Abby

have you tried using freeview? It is a lot more flexible than qdec and
supports a bunch of different color maps
cheers
Bruce


On Wed, 5 Jun 2019, Abby tang wrote:

>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to get some pictures about my results , so QDEC was used. 
> However I can't adjust thos
> e pictures which QDEC produced, such as picture1.
>
> When I read other's paper, they provided different pictures just like 
> picture2. If there any other m
> ethods to produce statistic pictures of brain? Can you give me some advices?
>
> Thank you for your help.
>
> Best regards
>
> Abby
>
>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] translations and rotations from an affine transform matrix

[Greve, Douglas N.,Ph.D.]

If it is an LTA (not .dat file), you can use
mri_coreg --mat2par ltafile
There will be 9 values that come out:
1-3: translation in mm
4-6: rotation in deg
7-9: should all be 1s in this case

On 6/20/2019 2:52 AM, Pfannmoeller, Joerg Peter wrote:
Hello,

is there a tool to extract the translations and rotations from an affine 
transform matrix (register.dof6.dat)?

Best Joerg



___
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

Re: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear Gwang-Won,
What version are you using? What’s the output of “recon-all –version”?
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Gwang-Won Kim 

Reply-To: Freesurfer support list 
Date: Friday, 21 June 2019 at 15:25
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."


External Email - Use Caution

Dear there,

I tried to process “Segmentation of thalamic nuclei” using source the 
FreeSurfer development version.
I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.
In two computer, there were massages “segmentThamicNuclei.sh: Command not 
found” and “bash: segmentThamicNuclei.sh: command not found”, respectively.
How do I resolve this problem?

Best,
Gwang-Won Kim

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] I have a question for "Segmentation of thalamic nuclei."

[Gwang-Won Kim]

External Email - Use CautionDear there, I tried to process “Segmentation of thalamic nuclei” using source the FreeSurfer development version.I filled out “segmentThalamicNuclei.sh  bert  [SUBJECTS_DIR]”.In two computer, there were massages “segmentThamicNuclei.sh: Command not found” and “bash: segmentThamicNuclei.sh: command not found”, respectively.How do I resolve this problem? Best,Gwang-Won Kim___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

Okay, thank you.

On Fri, Jun 21, 2019 at 2:24 PM Bruce Fischl 
wrote:

> Hi Shrabani
>
> I really don't know - I don't have any experience registering skulls.
> sorry
> Bruce
>
> On
> Fri, 21 Jun 2019, Shrabani Ghosh wrote:
>
> >
> > External Email - Use Caution
> >
> > I am using elastix. And I think it does something similar like ANTS. Do
> you think I should get the
> > proper output using elastix?
> >
> > On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh 
> wrote:
> >   Okay Thank You for your all the responses.
> >
> > On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Shrabani
> >
> >   you can read about FS on our wiki. We generally require a
> T1-weighted MRI
> >   as input and build models of lots of things from it (including
> skull, which
> >   will be more accurate if you also have a PD or T2-weighted image).
> >
> >   cheers
> >   Bruce
> >
> >
> >
> >
> >   On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > So in which case, freesurfer is applicable. Because I got a
> suggestion for CT to
> >   CT registration, I
> >   > can use freesurfer.
> >   > Thanks
> >   >
> >   > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> >   wrote:
> >   >   Hi Shrabani
> >   >
> >   >   no, that's not really what I'm saying. In any case, I'm
> not sure
> >   >   FreeSurfer is the right tool for you to use for this.
> >   >
> >   >   cheers
> >   >   Bruce
> >   >   On Fri, 21 Jun 2019,
> >   >   Shrabani Ghosh wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > So, you mean to say that two volumes need to be exactly
> same kind and
> >   having same
> >   >   information? So I
> >   >   > have generated a skull foramina model(which is
> triangular mesh) from the
> >   fixed image
> >   >   volume. Now I
> >   >   > want to register the model with a general patient data
> volume. But mesh
> >   and volume
> >   >   cannot be
> >   >   > registered so that I am trying to register the two
> volumes so that the
> >   model will warp
> >   >   on to the
> >   >   > patient data perfectly.
> >   >   >
> >   >   > regards
> >   >   > Shrabani Ghosh
> >   >   >
> >   >   > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl
> >wrote:
> >   >   >   not unless you also have an image of the whole
> brain. Even then
> >   I'm not
> >   >   >   sure it will do what you want, although I'm still
> not clear on
> >   exactly what
> >   >   >   you are doing. Registering one image of the skull
> to a model? Why?
> >   >   >
> >   >   >   On Fri, 21 Jun
> >   >   >   2019, Shrabani Ghosh wrote:
> >   >   >
> >   >   >   >
> >   >   >   > External Email - Use Caution
> >   >   >   >
> >   >   >   > These are skull images of axial representation.
> Can't I use
> >   freesurfer?
> >   >   Because here
> >   >   >   interpolation
> >   >   >   > is important.
> >   >   >   >
> >   >   >   > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl
> >   
> >   >   wrote:
> >   >   >   >   Hi Shrabani
> >   >   >   >
> >   >   >   >   I'm not even sure what these are images
> of. If you are
> >   looking for
> >   >   >   >   general-purpose registration tools you can
> try ANTS or
> >   something like
> >   >   that.
> >   >   >   >
> >   >   >   >   cheers
> >   >   >   >   Bruce
> >   >   >   >
> >   >   >   >
> >   >   >   >   On Fri, 21 Jun 2019, Shrabani
> >   >   >   >   Ghosh wrote:
> >   >   >   >
> >   >   >   >   >
> >   >   >   >   > External Email - Use
> Caution
> >   >   >   >   >
> >   >   >   >   > The fixed volume is my model volume and
> the other is a
> >   patient volume
> >   >   (moving
> >   >   >   )that I
> >   >   >   >   want to fit
> >   >   >   >   > and to the fixed volume. They are
> different in size and
> >   they have to
> >   >   be
> >   >   >   perfectly
> >   >   >   >   aligned. Please
> >   >   >   >   > guide me on how to do the
> registration. 8.png is the
> >   model volume.
> >   >   >   >

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

Hi Shrabani

I really don't know - I don't have any experience registering skulls. 
sorry

Bruce

On 
Fri, 21 Jun 2019, Shrabani Ghosh wrote:




External Email - Use Caution

I am using elastix. And I think it does something similar like ANTS. Do you 
think I should get the
proper output using elastix?

On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh  wrote:
  Okay Thank You for your all the responses. 

On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl  
wrote:
  Hi Shrabani

  you can read about FS on our wiki. We generally require a T1-weighted MRI
  as input and build models of lots of things from it (including skull, 
which
  will be more accurate if you also have a PD or T2-weighted image).

  cheers
  Bruce




  On Fri, 21 Jun 2019, Shrabani Ghosh wrote:

  >
  > External Email - Use Caution
  >
  > So in which case, freesurfer is applicable. Because I got a suggestion 
for CT to
  CT registration, I
  > can use freesurfer. 
  > Thanks
  >
  > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl 

  wrote:
  >       Hi Shrabani
  >
  >       no, that's not really what I'm saying. In any case, I'm not sure
  >       FreeSurfer is the right tool for you to use for this.
  >
  >       cheers
  >       Bruce
  >       On Fri, 21 Jun 2019,
  >       Shrabani Ghosh wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > So, you mean to say that two volumes need to be exactly same 
kind and
  having same
  >       information? So I
  >       > have generated a skull foramina model(which is triangular mesh) 
from the
  fixed image
  >       volume. Now I
  >       > want to register the model with a general patient data volume. 
But mesh
  and volume
  >       cannot be
  >       > registered so that I am trying to register the two volumes so 
that the
  model will warp
  >       on to the
  >       > patient data perfectly. 
  >       >
  >       > regards
  >       > Shrabani Ghosh
  >       >
  >       > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl
   wrote:
  >       >       not unless you also have an image of the whole brain. 
Even then
  I'm not
  >       >       sure it will do what you want, although I'm still not 
clear on
  exactly what
  >       >       you are doing. Registering one image of the skull to a 
model? Why?
  >       >
  >       >       On Fri, 21 Jun
  >       >       2019, Shrabani Ghosh wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > These are skull images of axial representation. Can't I 
use
  freesurfer?
  >       Because here
  >       >       interpolation
  >       >       > is important. 
  >       >       >
  >       >       > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl
  
  >       wrote:
  >       >       >       Hi Shrabani
  >       >       >
  >       >       >       I'm not even sure what these are images of. If 
you are
  looking for
  >       >       >       general-purpose registration tools you can try 
ANTS or
  something like
  >       that.
  >       >       >
  >       >       >       cheers
  >       >       >       Bruce
  >       >       >
  >       >       >
  >       >       >       On Fri, 21 Jun 2019, Shrabani
  >       >       >       Ghosh wrote:
  >       >       >
  >       >       >       >
  >       >       >       > External Email - Use Caution
  >       >       >       >
  >       >       >       > The fixed volume is my model volume and the 
other is a
  patient volume
  >       (moving
  >       >       )that I
  >       >       >       want to fit
  >       >       >       > and to the fixed volume. They are different in 
size and
  they have to
  >       be
  >       >       perfectly
  >       >       >       aligned. Please
  >       >       >       > guide me on how to do the registration. 8.png 
is the
  model volume. 
  >       >       >       > 9.png is the patient volume. 
  >       >       >       > 10.png is the outline of their size. the 
smaller one is
  the moving
  >       image and
  >       >       the
  >       >       >       bigger one is the
  >       >       >       > fixed image. 
  >       >       >       >
  >       >       >       > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl
  >       
  >       >       wrote:
  >       >       >       >       what kinds of volumes are they and why 
are you
  registering them?
  >       >       >       >       cheers
  >       >       >      

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

I am using elastix. And I think it does something similar like ANTS. Do you
think I should get the proper output using elastix?

On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh 
wrote:

> Okay Thank You for your all the responses.
>
> On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl 
> wrote:
>
>> Hi Shrabani
>>
>> you can read about FS on our wiki. We generally require a T1-weighted MRI
>> as input and build models of lots of things from it (including skull,
>> which
>> will be more accurate if you also have a PD or T2-weighted image).
>>
>> cheers
>> Bruce
>>
>>
>>
>>
>> On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > So in which case, freesurfer is applicable. Because I got a suggestion
>> for CT to CT registration, I
>> > can use freesurfer.
>> > Thanks
>> >
>> > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   Hi Shrabani
>> >
>> >   no, that's not really what I'm saying. In any case, I'm not sure
>> >   FreeSurfer is the right tool for you to use for this.
>> >
>> >   cheers
>> >   Bruce
>> >   On Fri, 21 Jun 2019,
>> >   Shrabani Ghosh wrote:
>> >
>> >   >
>> >   > External Email - Use Caution
>> >   >
>> >   > So, you mean to say that two volumes need to be exactly same
>> kind and having same
>> >   information? So I
>> >   > have generated a skull foramina model(which is triangular mesh)
>> from the fixed image
>> >   volume. Now I
>> >   > want to register the model with a general patient data volume.
>> But mesh and volume
>> >   cannot be
>> >   > registered so that I am trying to register the two volumes so
>> that the model will warp
>> >   on to the
>> >   > patient data perfectly.
>> >   >
>> >   > regards
>> >   > Shrabani Ghosh
>> >   >
>> >   > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   >   not unless you also have an image of the whole brain.
>> Even then I'm not
>> >   >   sure it will do what you want, although I'm still not
>> clear on exactly what
>> >   >   you are doing. Registering one image of the skull to a
>> model? Why?
>> >   >
>> >   >   On Fri, 21 Jun
>> >   >   2019, Shrabani Ghosh wrote:
>> >   >
>> >   >   >
>> >   >   > External Email - Use Caution
>> >   >   >
>> >   >   > These are skull images of axial representation. Can't I
>> use freesurfer?
>> >   Because here
>> >   >   interpolation
>> >   >   > is important.
>> >   >   >
>> >   >   > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> >   wrote:
>> >   >   >   Hi Shrabani
>> >   >   >
>> >   >   >   I'm not even sure what these are images of. If
>> you are looking for
>> >   >   >   general-purpose registration tools you can try
>> ANTS or something like
>> >   that.
>> >   >   >
>> >   >   >   cheers
>> >   >   >   Bruce
>> >   >   >
>> >   >   >
>> >   >   >   On Fri, 21 Jun 2019, Shrabani
>> >   >   >   Ghosh wrote:
>> >   >   >
>> >   >   >   >
>> >   >   >   > External Email - Use Caution
>> >   >   >   >
>> >   >   >   > The fixed volume is my model volume and the
>> other is a patient volume
>> >   (moving
>> >   >   )that I
>> >   >   >   want to fit
>> >   >   >   > and to the fixed volume. They are different in
>> size and they have to
>> >   be
>> >   >   perfectly
>> >   >   >   aligned. Please
>> >   >   >   > guide me on how to do the registration. 8.png
>> is the model volume.
>> >   >   >   > 9.png is the patient volume.
>> >   >   >   > 10.png is the outline of their size. the
>> smaller one is the moving
>> >   image and
>> >   >   the
>> >   >   >   bigger one is the
>> >   >   >   > fixed image.
>> >   >   >   >
>> >   >   >   > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl
>> >   
>> >   >   wrote:
>> >   >   >   >   what kinds of volumes are they and why
>> are you registering them?
>> >   >   >   >   cheers
>> >   >   >   >   Bruce
>> >   >   >   >   On Thu, 20
>> >   >   >   >   Jun 2019, Shrabani Ghosh wrote:
>> >   >   >   >
>> >   >   >   >   >
>> >   >   >   >   > External Email - Use
>> Caution
>> >   >   >   >   >
>> >   >   >   >   > Hi freesurfer,
>> >   >   >   >   > I want to do registration on two image
>> v

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

Okay Thank You for your all the responses.

On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl 
wrote:

> Hi Shrabani
>
> you can read about FS on our wiki. We generally require a T1-weighted MRI
> as input and build models of lots of things from it (including skull,
> which
> will be more accurate if you also have a PD or T2-weighted image).
>
> cheers
> Bruce
>
>
>
>
> On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
>
> >
> > External Email - Use Caution
> >
> > So in which case, freesurfer is applicable. Because I got a suggestion
> for CT to CT registration, I
> > can use freesurfer.
> > Thanks
> >
> > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Shrabani
> >
> >   no, that's not really what I'm saying. In any case, I'm not sure
> >   FreeSurfer is the right tool for you to use for this.
> >
> >   cheers
> >   Bruce
> >   On Fri, 21 Jun 2019,
> >   Shrabani Ghosh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > So, you mean to say that two volumes need to be exactly same
> kind and having same
> >   information? So I
> >   > have generated a skull foramina model(which is triangular mesh)
> from the fixed image
> >   volume. Now I
> >   > want to register the model with a general patient data volume.
> But mesh and volume
> >   cannot be
> >   > registered so that I am trying to register the two volumes so
> that the model will warp
> >   on to the
> >   > patient data perfectly.
> >   >
> >   > regards
> >   > Shrabani Ghosh
> >   >
> >   > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   >   not unless you also have an image of the whole brain. Even
> then I'm not
> >   >   sure it will do what you want, although I'm still not
> clear on exactly what
> >   >   you are doing. Registering one image of the skull to a
> model? Why?
> >   >
> >   >   On Fri, 21 Jun
> >   >   2019, Shrabani Ghosh wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > These are skull images of axial representation. Can't I
> use freesurfer?
> >   Because here
> >   >   interpolation
> >   >   > is important.
> >   >   >
> >   >   > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> >   wrote:
> >   >   >   Hi Shrabani
> >   >   >
> >   >   >   I'm not even sure what these are images of. If you
> are looking for
> >   >   >   general-purpose registration tools you can try
> ANTS or something like
> >   that.
> >   >   >
> >   >   >   cheers
> >   >   >   Bruce
> >   >   >
> >   >   >
> >   >   >   On Fri, 21 Jun 2019, Shrabani
> >   >   >   Ghosh wrote:
> >   >   >
> >   >   >   >
> >   >   >   > External Email - Use Caution
> >   >   >   >
> >   >   >   > The fixed volume is my model volume and the
> other is a patient volume
> >   (moving
> >   >   )that I
> >   >   >   want to fit
> >   >   >   > and to the fixed volume. They are different in
> size and they have to
> >   be
> >   >   perfectly
> >   >   >   aligned. Please
> >   >   >   > guide me on how to do the registration. 8.png is
> the model volume.
> >   >   >   > 9.png is the patient volume.
> >   >   >   > 10.png is the outline of their size. the smaller
> one is the moving
> >   image and
> >   >   the
> >   >   >   bigger one is the
> >   >   >   > fixed image.
> >   >   >   >
> >   >   >   > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl
> >   
> >   >   wrote:
> >   >   >   >   what kinds of volumes are they and why are
> you registering them?
> >   >   >   >   cheers
> >   >   >   >   Bruce
> >   >   >   >   On Thu, 20
> >   >   >   >   Jun 2019, Shrabani Ghosh wrote:
> >   >   >   >
> >   >   >   >   >
> >   >   >   >   > External Email - Use
> Caution
> >   >   >   >   >
> >   >   >   >   > Hi freesurfer,
> >   >   >   >   > I want to do registration on two image
> volumes nifti file.
> >   What are
> >   >   the
> >   >   >   commands I
> >   >   >   >   have to use to do
> >   >   >   >   > the registration?
> >   >   >   >   >
> >   >   >   >   > Shrabani Ghosh
> >   >   >   >   >
>

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

Hi Shrabani

you can read about FS on our wiki. We generally require a T1-weighted MRI 
as input and build models of lots of things from it (including skull, which 
will be more accurate if you also have a PD or T2-weighted image).


cheers
Bruce




On Fri, 21 Jun 2019, Shrabani Ghosh wrote:



External Email - Use Caution

So in which case, freesurfer is applicable. Because I got a suggestion for CT 
to CT registration, I
can use freesurfer. 
Thanks

On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl  
wrote:
  Hi Shrabani

  no, that's not really what I'm saying. In any case, I'm not sure
  FreeSurfer is the right tool for you to use for this.

  cheers
  Bruce
  On Fri, 21 Jun 2019,
  Shrabani Ghosh wrote:

  >
  > External Email - Use Caution
  >
  > So, you mean to say that two volumes need to be exactly same kind and 
having same
  information? So I
  > have generated a skull foramina model(which is triangular mesh) from 
the fixed image
  volume. Now I
  > want to register the model with a general patient data volume. But mesh 
and volume
  cannot be
  > registered so that I am trying to register the two volumes so that the 
model will warp
  on to the
  > patient data perfectly. 
  >
  > regards
  > Shrabani Ghosh
  >
  > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl 
 wrote:
  >       not unless you also have an image of the whole brain. Even then 
I'm not
  >       sure it will do what you want, although I'm still not clear on 
exactly what
  >       you are doing. Registering one image of the skull to a model? Why?
  >
  >       On Fri, 21 Jun
  >       2019, Shrabani Ghosh wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > These are skull images of axial representation. Can't I use 
freesurfer?
  Because here
  >       interpolation
  >       > is important. 
  >       >
  >       > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl 

  wrote:
  >       >       Hi Shrabani
  >       >
  >       >       I'm not even sure what these are images of. If you are 
looking for
  >       >       general-purpose registration tools you can try ANTS or 
something like
  that.
  >       >
  >       >       cheers
  >       >       Bruce
  >       >
  >       >
  >       >       On Fri, 21 Jun 2019, Shrabani
  >       >       Ghosh wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > The fixed volume is my model volume and the other is a 
patient volume
  (moving
  >       )that I
  >       >       want to fit
  >       >       > and to the fixed volume. They are different in size and 
they have to
  be
  >       perfectly
  >       >       aligned. Please
  >       >       > guide me on how to do the registration. 8.png is the 
model volume. 
  >       >       > 9.png is the patient volume. 
  >       >       > 10.png is the outline of their size. the smaller one is 
the moving
  image and
  >       the
  >       >       bigger one is the
  >       >       > fixed image. 
  >       >       >
  >       >       > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl
  
  >       wrote:
  >       >       >       what kinds of volumes are they and why are you 
registering them?
  >       >       >       cheers
  >       >       >       Bruce
  >       >       >       On Thu, 20
  >       >       >       Jun 2019, Shrabani Ghosh wrote:
  >       >       >
  >       >       >       >
  >       >       >       > External Email - Use Caution
  >       >       >       >
  >       >       >       > Hi freesurfer,
  >       >       >       > I want to do registration on two image volumes 
nifti file.
  What are
  >       the
  >       >       commands I
  >       >       >       have to use to do
  >       >       >       > the registration?
  >       >       >       >
  >       >       >       > Shrabani Ghosh
  >       >       >       >
  >       >       >       >___
  >       >       >       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
  >       >
  >       >
  >       >___

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

So in which case, freesurfer is applicable. Because I got a suggestion for
CT to CT registration, I can use freesurfer.

Thanks

On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl 
wrote:

> Hi Shrabani
>
> no, that's not really what I'm saying. In any case, I'm not sure
> FreeSurfer is the right tool for you to use for this.
>
> cheers
> Bruce
> On Fri, 21 Jun 2019,
> Shrabani Ghosh wrote:
>
> >
> > External Email - Use Caution
> >
> > So, you mean to say that two volumes need to be exactly same kind and
> having same information? So I
> > have generated a skull foramina model(which is triangular mesh) from the
> fixed image volume. Now I
> > want to register the model with a general patient data volume. But mesh
> and volume cannot be
> > registered so that I am trying to register the two volumes so that the
> model will warp on to the
> > patient data perfectly.
> >
> > regards
> > Shrabani Ghosh
> >
> > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   not unless you also have an image of the whole brain. Even then
> I'm not
> >   sure it will do what you want, although I'm still not clear on
> exactly what
> >   you are doing. Registering one image of the skull to a model? Why?
> >
> >   On Fri, 21 Jun
> >   2019, Shrabani Ghosh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > These are skull images of axial representation. Can't I use
> freesurfer? Because here
> >   interpolation
> >   > is important.
> >   >
> >   > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   >   Hi Shrabani
> >   >
> >   >   I'm not even sure what these are images of. If you are
> looking for
> >   >   general-purpose registration tools you can try ANTS or
> something like that.
> >   >
> >   >   cheers
> >   >   Bruce
> >   >
> >   >
> >   >   On Fri, 21 Jun 2019, Shrabani
> >   >   Ghosh wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > The fixed volume is my model volume and the other is a
> patient volume (moving
> >   )that I
> >   >   want to fit
> >   >   > and to the fixed volume. They are different in size and
> they have to be
> >   perfectly
> >   >   aligned. Please
> >   >   > guide me on how to do the registration. 8.png is the
> model volume.
> >   >   > 9.png is the patient volume.
> >   >   > 10.png is the outline of their size. the smaller one is
> the moving image and
> >   the
> >   >   bigger one is the
> >   >   > fixed image.
> >   >   >
> >   >   > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> >   wrote:
> >   >   >   what kinds of volumes are they and why are you
> registering them?
> >   >   >   cheers
> >   >   >   Bruce
> >   >   >   On Thu, 20
> >   >   >   Jun 2019, Shrabani Ghosh wrote:
> >   >   >
> >   >   >   >
> >   >   >   > External Email - Use Caution
> >   >   >   >
> >   >   >   > Hi freesurfer,
> >   >   >   > I want to do registration on two image volumes
> nifti file. What are
> >   the
> >   >   commands I
> >   >   >   have to use to do
> >   >   >   > the registration?
> >   >   >   >
> >   >   >   > Shrabani Ghosh
> >   >   >   >
> >   >   >   >___
> >   >   >   Freesurfer mailing list
> >   >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >   >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >   >
> >   >   >
> >   >   >___
> >   >   Freesurfer mailing list
> >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> 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

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

Hi Shrabani

no, that's not really what I'm saying. In any case, I'm not sure 
FreeSurfer is the right tool for you to use for this.


cheers
Bruce
On Fri, 21 Jun 2019, 
Shrabani Ghosh wrote:




External Email - Use Caution

So, you mean to say that two volumes need to be exactly same kind and having 
same information? So I
have generated a skull foramina model(which is triangular mesh) from the fixed 
image volume. Now I
want to register the model with a general patient data volume. But mesh and 
volume cannot be
registered so that I am trying to register the two volumes so that the model 
will warp on to the
patient data perfectly. 

regards
Shrabani Ghosh

On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl  
wrote:
  not unless you also have an image of the whole brain. Even then I'm not
  sure it will do what you want, although I'm still not clear on exactly 
what
  you are doing. Registering one image of the skull to a model? Why?

  On Fri, 21 Jun
  2019, Shrabani Ghosh wrote:

  >
  > External Email - Use Caution
  >
  > These are skull images of axial representation. Can't I use freesurfer? 
Because here
  interpolation
  > is important. 
  >
  > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl 
 wrote:
  >       Hi Shrabani
  >
  >       I'm not even sure what these are images of. If you are looking for
  >       general-purpose registration tools you can try ANTS or something 
like that.
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Fri, 21 Jun 2019, Shrabani
  >       Ghosh wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > The fixed volume is my model volume and the other is a patient 
volume (moving
  )that I
  >       want to fit
  >       > and to the fixed volume. They are different in size and they 
have to be
  perfectly
  >       aligned. Please
  >       > guide me on how to do the registration. 8.png is the model 
volume. 
  >       > 9.png is the patient volume. 
  >       > 10.png is the outline of their size. the smaller one is the 
moving image and
  the
  >       bigger one is the
  >       > fixed image. 
  >       >
  >       > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl 

  wrote:
  >       >       what kinds of volumes are they and why are you 
registering them?
  >       >       cheers
  >       >       Bruce
  >       >       On Thu, 20
  >       >       Jun 2019, Shrabani Ghosh wrote:
  >       >
  >       >       >
  >       >       > External Email - Use Caution
  >       >       >
  >       >       > Hi freesurfer,
  >       >       > I want to do registration on two image volumes nifti 
file. What are
  the
  >       commands I
  >       >       have to use to do
  >       >       > the registration?
  >       >       >
  >       >       > Shrabani Ghosh
  >       >       >
  >       >       >___
  >       >       Freesurfer mailing list
  >       >       Freesurfer@nmr.mgh.harvard.edu
  >       >       
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >       >
  >       >
  >       >___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] WARNING: no voxels in AR1 computation

[Francesca Pentimalli]

External Email - Use Caution

Dear FreeSurfer experts,

I am trying to run *mri_glmfit *on a series of concatenated volumes.

mri_glmfit --y $SUBJECTS_DIR/concat/new_glm_input.mgh --fsgd Qdec/qdec.fsgd
--mask fsaverage/label_volume/mask.mgz --glmdir glm_output --C
$SUBJECTS_DIR/qdec/Untitled/contrasts/lh-Avg-Intercept-volume.mat

I am getting the following : WARNING: no voxels in AR1 computation.  I am
guessing that this is due to the results of the analysis, or is this
potentially a problem with the specific contrast used? If so, what should
be kept in mind while creating new contrasts?

Regards,
Francesca

*Francesca Pentimalli Biscaretti di Ruffia *
Via S. Eufemia 3, 35121 Padova (Italy)
Mobile: +39 3483862788
francesca.pentimallibiscarettidiruf...@studenti.unipd.it
fpentimalli...@gmail.com
fpe...@mit.edu
fp...@bu.edu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

So, you mean to say that two volumes need to be exactly same kind and
having same information?
So I have generated a skull foramina model(which is triangular mesh) from
the fixed image volume. Now I want to register the model with a general
patient data volume. But mesh and volume cannot be registered so that I am
trying to register the two volumes so that the model will warp on to the
patient data perfectly.

regards
Shrabani Ghosh

On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl 
wrote:

> not unless you also have an image of the whole brain. Even then I'm not
> sure it will do what you want, although I'm still not clear on exactly
> what
> you are doing. Registering one image of the skull to a model? Why?
>
> On Fri, 21 Jun
> 2019, Shrabani Ghosh wrote:
>
> >
> > External Email - Use Caution
> >
> > These are skull images of axial representation. Can't I use freesurfer?
> Because here interpolation
> > is important.
> >
> > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Shrabani
> >
> >   I'm not even sure what these are images of. If you are looking for
> >   general-purpose registration tools you can try ANTS or something
> like that.
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Fri, 21 Jun 2019, Shrabani
> >   Ghosh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > The fixed volume is my model volume and the other is a patient
> volume (moving )that I
> >   want to fit
> >   > and to the fixed volume. They are different in size and they
> have to be perfectly
> >   aligned. Please
> >   > guide me on how to do the registration. 8.png is the model
> volume.
> >   > 9.png is the patient volume.
> >   > 10.png is the outline of their size. the smaller one is the
> moving image and the
> >   bigger one is the
> >   > fixed image.
> >   >
> >   > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   >   what kinds of volumes are they and why are you registering
> them?
> >   >   cheers
> >   >   Bruce
> >   >   On Thu, 20
> >   >   Jun 2019, Shrabani Ghosh wrote:
> >   >
> >   >   >
> >   >   > External Email - Use Caution
> >   >   >
> >   >   > Hi freesurfer,
> >   >   > I want to do registration on two image volumes nifti
> file. What are the
> >   commands I
> >   >   have to use to do
> >   >   > the registration?
> >   >   >
> >   >   > Shrabani Ghosh
> >   >   >
> >   >   >___
> >   >   Freesurfer mailing list
> >   >   Freesurfer@nmr.mgh.harvard.edu
> >   >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

not unless you also have an image of the whole brain. Even then I'm not 
sure it will do what you want, although I'm still not clear on exactly what 
you are doing. Registering one image of the skull to a model? Why?


On Fri, 21 Jun 
2019, Shrabani Ghosh wrote:




External Email - Use Caution

These are skull images of axial representation. Can't I use freesurfer? Because 
here interpolation
is important. 

On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl  
wrote:
  Hi Shrabani

  I'm not even sure what these are images of. If you are looking for
  general-purpose registration tools you can try ANTS or something like 
that.

  cheers
  Bruce


  On Fri, 21 Jun 2019, Shrabani
  Ghosh wrote:

  >
  > External Email - Use Caution
  >
  > The fixed volume is my model volume and the other is a patient volume 
(moving )that I
  want to fit
  > and to the fixed volume. They are different in size and they have to be 
perfectly
  aligned. Please
  > guide me on how to do the registration. 8.png is the model volume. 
  > 9.png is the patient volume. 
  > 10.png is the outline of their size. the smaller one is the moving 
image and the
  bigger one is the
  > fixed image. 
  >
  > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl 
 wrote:
  >       what kinds of volumes are they and why are you registering them?
  >       cheers
  >       Bruce
  >       On Thu, 20
  >       Jun 2019, Shrabani Ghosh wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hi freesurfer,
  >       > I want to do registration on two image volumes nifti file. What 
are the
  commands I
  >       have to use to do
  >       > the registration?
  >       >
  >       > Shrabani Ghosh
  >       >
  >       >___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration of image volumes

[Shrabani Ghosh]

External Email - Use Caution

These are skull images of axial representation. Can't I use freesurfer?
Because here interpolation is important.

On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl 
wrote:

> Hi Shrabani
>
> I'm not even sure what these are images of. If you are looking for
> general-purpose registration tools you can try ANTS or something like that.
>
> cheers
> Bruce
>
>
> On Fri, 21 Jun 2019, Shrabani
> Ghosh wrote:
>
> >
> > External Email - Use Caution
> >
> > The fixed volume is my model volume and the other is a patient volume
> (moving )that I want to fit
> > and to the fixed volume. They are different in size and they have to be
> perfectly aligned. Please
> > guide me on how to do the registration. 8.png is the model volume.
> > 9.png is the patient volume.
> > 10.png is the outline of their size. the smaller one is the moving image
> and the bigger one is the
> > fixed image.
> >
> > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   what kinds of volumes are they and why are you registering them?
> >   cheers
> >   Bruce
> >   On Thu, 20
> >   Jun 2019, Shrabani Ghosh wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi freesurfer,
> >   > I want to do registration on two image volumes nifti file. What
> are the commands I
> >   have to use to do
> >   > the registration?
> >   >
> >   > Shrabani Ghosh
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

Hi Shrabani

I'm not even sure what these are images of. If you are looking for 
general-purpose registration tools you can try ANTS or something like that.


cheers
Bruce


On Fri, 21 Jun 2019, Shrabani 
Ghosh wrote:




External Email - Use Caution

The fixed volume is my model volume and the other is a patient volume (moving 
)that I want to fit
and to the fixed volume. They are different in size and they have to be 
perfectly aligned. Please
guide me on how to do the registration. 8.png is the model volume. 
9.png is the patient volume. 
10.png is the outline of their size. the smaller one is the moving image and 
the bigger one is the
fixed image. 

On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl  
wrote:
  what kinds of volumes are they and why are you registering them?
  cheers
  Bruce
  On Thu, 20
  Jun 2019, Shrabani Ghosh wrote:

  >
  > External Email - Use Caution
  >
  > Hi freesurfer,
  > I want to do registration on two image volumes nifti file. What are the 
commands I
  have to use to do
  > the registration?
  >
  > Shrabani Ghosh
  >
  >___
  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

Re: [Freesurfer] Labelling SurfStat p-value surface map

[Bruce Fischl]

I don't think it matters but I would use eye instead of nan for M. But the 
critical issue is where you get your data and what dimensions it has

cheers
Bruce

On Fri, 21 Jun 2019, Loïc Daumail wrote:



External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4);
save_mgh('freeview_overlay', 
['/home/loic/Documents/emb_output/mgh_format/lh_emb_'
char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);
 
Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail  a écrit :
  Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an error...
I have a matrix of 18715 elements regarding both hemispheres.
The size of fsaverage5 is 20484 I believe, so I filled the remaining elements 
with zeros, and
also tried with rand().

The other issue is that I am not so sure which part of the matrix is for lh and 
the other one
for rh. Thus, I divided 18715/2 and took the 9357 first elements of the 18715 
matrix. Then
filled it with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with freeview using 
the following
command line:
freeview 
-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh
_format/lh_emb_sub-002_compassion.mgz

I am getting the following error:
"
Did not find any volume info
2 [0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access
out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR:
or try http://valgrind.org on linux or man libgmalloc on Apple to find memory 
corruption
errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG
revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic Fri 
Jun 21 12:15:53
2019
[0]PETSC ERROR: Libraries linked 
from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin
ux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 
FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc



Le jeu. 20 juin 2019 à 19:39, Bruce Fischl  a écrit 
:
  Hi Loïc

  the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
  know it is a surface overlay I believe

  cheers
  Bruce



  On Thu, 20 Jun 2019, Loïc Daumail wrote:

  >
  > External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I am reaching out to you, as I am trying to load the surface scalar 
values of
  diffusion embedding
  > for overlay on a pial surface in Freeview.
  >
  > I used save_mgh to save a scalar matrix containing surface embedding 
values in
  an .mgz format.
  > However I can't load it in freeview, be either only half of the matrix 
data (one
  hemisphere I
  > assume) or the whole matrix saved in the same file.
  >
  > Is there anything specific I need to do in order to be able to 
visualize a
  scalar overlay on a
  > surface? Is .mgz a wrong format for scalar values? I also tried with 
.nii.gz, or
  .mgh. I am not even
  > sure save_mgh can do all this...
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  >
  >
  > Le lun. 27 mai 2019 à 11:54, Loïc Daumail  a 
écrit :
  >       Hi Tim,
  >
  > Your link works perfectly, it's awesome!
  > Thanks a lot,
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:43, Loïc Daumail  a 
écri

Re: [Freesurfer] voxel coordinates of corpus collosum

[Bruce Fischl]

can you send us the full command line and screen output? Doug might have 
an easy way to do it, but personally I would do it in matlab

cheers
Bruce
On Fri, 21 Jun 
2019, Sadia Sheikh wrote:




External Email - Use Caution

Thanks for your reply. I want to get the voxel coordinates of  CC and its 
subregions. I tried using
the command mri_vol2label for cc subregions also. But still I am getting the 
error message: found no
voxels matching id 251.
What is the right command to get the coordinates of CC?

Thanks in advance.
Sadia
 

On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl  
wrote:
  Hi Sadia

  we subdivide the cc into multiple components:

  251 CC_Posterior                            0   0   64  0
  252 CC_Mid_Posterior                        0   0   112 0
  253 CC_Central                              0   0   160 0
  254 CC_Mid_Anterior                         0   0   208 0
  255 CC_Anterior                             0   0   255 0


  cheers
  Bruce

  On Thu, 20 Jun
  2019, Sadia
  Sheikh wrote:

  >
  > External Email - Use Caution
  >
  > Dear Freesurfer experts
  > How can I get the voxel coordinates of the segmented corpus callosum? I 
tried using
  the command
  > mri_vol2label and id of the corpus callosum as 192  as given in 
Freesurfer LUT, 
  > but it gives an error: found no voxels matching id 192 
  >
  > Thanks in advance
  >
  > Sadia
  >
  >___
  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

Re: [Freesurfer] Labelling SurfStat p-value surface map

[Bruce Fischl]

why do you have 18715 elements? How did you create it? You can run mri_info 
on the .mgz volume to see if it has the correct dimensions.


BTW: you might repost your original question early next week if you haven't 
resolve things. Doug is back and probably has an easy way to do what you 
want


cheers
Bruce


On Fri, 21 Jun 2019, 
Loïc Daumail wrote:




External Email - Use Caution

Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an error...
I have a matrix of 18715 elements regarding both hemispheres.
The size of fsaverage5 is 20484 I believe, so I filled the remaining elements 
with zeros, and also
tried with rand().

The other issue is that I am not so sure which part of the matrix is for lh and 
the other one for
rh. Thus, I divided 18715/2 and took the 9357 first elements of the 18715 
matrix. Then filled it
with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with freeview using 
the following
command line:
freeview 
-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh
_format/lh_emb_sub-002_compassion.mgz

I am getting the following error:
"
Did not find any volume info
2 [0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of
range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or
try http://valgrind.org on linux or man libgmalloc on Apple to find memory 
corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision:
4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic Fri 
Jun 21 12:15:53 2019
[0]PETSC ERROR: Libraries linked 
from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin
ux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0
--with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc



Le jeu. 20 juin 2019 à 19:39, Bruce Fischl  a écrit 
:
  Hi Loïc

  the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
  know it is a surface overlay I believe

  cheers
  Bruce



  On Thu, 20 Jun 2019, Loïc Daumail wrote:

  >
  > External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I am reaching out to you, as I am trying to load the surface scalar 
values of
  diffusion embedding
  > for overlay on a pial surface in Freeview.
  >
  > I used save_mgh to save a scalar matrix containing surface embedding 
values in an .mgz
  format.
  > However I can't load it in freeview, be either only half of the matrix 
data (one
  hemisphere I
  > assume) or the whole matrix saved in the same file.
  >
  > Is there anything specific I need to do in order to be able to 
visualize a scalar
  overlay on a
  > surface? Is .mgz a wrong format for scalar values? I also tried with 
.nii.gz, or .mgh.
  I am not even
  > sure save_mgh can do all this...
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  >
  >
  > Le lun. 27 mai 2019 à 11:54, Loïc Daumail  a 
écrit :
  >       Hi Tim,
  >
  > Your link works perfectly, it's awesome!
  > Thanks a lot,
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:43, Loïc Daumail  a 
écrit :
  >       Hi Tim,
  >
  > 'mean_rest' is a diffusion embedding map, which contains scores for 
every vertex on
  > fsaverage5 surfa

Re: [Freesurfer] Registration of image volumes

[Bruce Fischl]

what kinds of volumes are they and why are you registering them?
cheers
Bruce
On Thu, 20 
Jun 2019, Shrabani Ghosh wrote:




External Email - Use Caution

Hi freesurfer,
I want to do registration on two image volumes nifti file. What are the 
commands I have to use to do
the registration?

Shrabani Ghosh

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Problem with installation test

[Bruce Fischl]

if you have multiple cores you can use -openmp  which gives a pretty 
good speed increase up to about N=4 or 5


cheers
Bruce
On Thu, 20 Jun 2019, Shrabani Ghosh 
wrote:




External Email - Use Caution

Thank You. It's working now. But I can see the execution time is really slow. 
Is it possible to make
it faster using CUDA or any other way?

On Thu, Jun 20, 2019 at 1:29 AM fsbuild  wrote:
  Hello Shrabani,
It looks like you do not have tcsh installed on your machine to run recon-all 
which is a tcsh
script,

If you are using RedHat/CentOS linux,

$ sudo yum install tcsh

Fedora linux

$ sudo dnf install tcsh

Ubuntu/debian linux,

$ sudo apt-get install tcsh

I would also probably install csh the same way as well.

- R.


  On Jun 19, 2019, at 20:49, Shrabani Ghosh  wrote:

External Email - Use Caution


Hi  freesurfer, 
I am following the installation test as suggested (

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall  and am
currently stuck at example 2. When I ran recon-all, I got the output: 


"bash: /home/sghos003/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter:

 No such file or directory"

Any suggestions? Thank you.

Shrabani Ghosh

___
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

Re: [Freesurfer] Labelling SurfStat p-value surface map

[Loïc Daumail]

External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4);
save_mgh('freeview_overlay',
['/home/loic/Documents/emb_output/mgh_format/lh_emb_' char(subjectsList(1))
'_' char(statesList(1)) '.mgz'], M);

Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail  a
écrit :

> Hi Bruce,
>
> Thanks for your tip. Unfortunately, I am still running through an error...
> I have a matrix of 18715 elements regarding both hemispheres.
> The size of fsaverage5 is 20484 I believe, so I filled the remaining
> elements with zeros, and also tried with rand().
>
> The other issue is that I am not so sure which part of the matrix is for
> lh and the other one for rh. Thus, I divided 18715/2 and took the 9357
> first elements of the 18715 matrix. Then filled it with zeros or random
> values to reach 10242.
>
> Then I saved it with save_mgh function and tried to load it with freeview
> using the following command line:
> freeview -f
> ~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh_format/lh_emb_sub-002_compassion.mgz
>
> I am getting the following error:
> "
> Did not find any volume info
> 2 [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic
> Fri Jun 21 12:15:53 2019
> [0]PETSC ERROR: Libraries linked from
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"
>
> Any idea of what could be wrong in my process?
>
> Thanks
>
> Sincerely,
>
> Loïc
>
>
>
> Le jeu. 20 juin 2019 à 19:39, Bruce Fischl  a
> écrit :
>
>> Hi Loïc
>>
>> the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
>> know it is a surface overlay I believe
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 20 Jun 2019, Loïc Daumail wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hi Bruce,
>> >
>> > I am reaching out to you, as I am trying to load the surface scalar
>> values of diffusion embedding
>> > for overlay on a pial surface in Freeview.
>> >
>> > I used save_mgh to save a scalar matrix containing surface embedding
>> values in an .mgz format.
>> > However I can't load it in freeview, be either only half of the matrix
>> data (one hemisphere I
>> > assume) or the whole matrix saved in the same file.
>> >
>> > Is there anything specific I need to do in order to be able to
>> visualize a scalar overlay on a
>> > surface? Is .mgz a wrong format for scalar values? I also tried with
>> .nii.gz, or .mgh. I am not even
>> > sure save_mgh can do all this...
>> >
>> > Thanks in advance,
>> >
>> > Sincerely,
>> >
>> > Loïc
>> >
>> >
>> >
>> > Le lun. 27 mai 2019 à 11:54, Loïc Daumail  a
>> écrit :
>> >   Hi Tim,
>> >
>> > Your link works perfectly, it's awesome!
>> > Thanks a lot,
>> >
>> > Best,
>> >
>> > Loïc
>> >
>> > Le lun. 27 mai 2019 à 11:43, Loïc Daumail  a
>> écrit :
>> >   Hi Tim,
>> >
>> > 'mean_rest' is a diffusion embedding map, which contains scores for
>> every vertex on
>> > fsaverage5 surface resolution.
>> > 'surf.b' is the pial surface of both hemispheres of fsaverage5... I
>>

Re: [Freesurfer] Labelling SurfStat p-value surface map

[Loïc Daumail]

External Email - Use Caution

Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an error...
I have a matrix of 18715 elements regarding both hemispheres.
The size of fsaverage5 is 20484 I believe, so I filled the remaining
elements with zeros, and also tried with rand().

The other issue is that I am not so sure which part of the matrix is for lh
and the other one for rh. Thus, I divided 18715/2 and took the 9357 first
elements of the 18715 matrix. Then filled it with zeros or random values to
reach 10242.

Then I saved it with save_mgh function and tried to load it with freeview
using the following command line:
freeview -f
~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh_format/lh_emb_sub-002_compassion.mgz

I am getting the following error:
"
Did not find any volume info
2 [0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic
Fri Jun 21 12:15:53 2019
[0]PETSC ERROR: Libraries linked from
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc



Le jeu. 20 juin 2019 à 19:39, Bruce Fischl  a
écrit :

> Hi Loïc
>
> the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
> know it is a surface overlay I believe
>
> cheers
> Bruce
>
>
>
> On Thu, 20 Jun 2019, Loïc Daumail wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > I am reaching out to you, as I am trying to load the surface scalar
> values of diffusion embedding
> > for overlay on a pial surface in Freeview.
> >
> > I used save_mgh to save a scalar matrix containing surface embedding
> values in an .mgz format.
> > However I can't load it in freeview, be either only half of the matrix
> data (one hemisphere I
> > assume) or the whole matrix saved in the same file.
> >
> > Is there anything specific I need to do in order to be able to visualize
> a scalar overlay on a
> > surface? Is .mgz a wrong format for scalar values? I also tried with
> .nii.gz, or .mgh. I am not even
> > sure save_mgh can do all this...
> >
> > Thanks in advance,
> >
> > Sincerely,
> >
> > Loïc
> >
> >
> >
> > Le lun. 27 mai 2019 à 11:54, Loïc Daumail  a
> écrit :
> >   Hi Tim,
> >
> > Your link works perfectly, it's awesome!
> > Thanks a lot,
> >
> > Best,
> >
> > Loïc
> >
> > Le lun. 27 mai 2019 à 11:43, Loïc Daumail  a
> écrit :
> >   Hi Tim,
> >
> > 'mean_rest' is a diffusion embedding map, which contains scores for
> every vertex on
> > fsaverage5 surface resolution.
> > 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also
> tried forjust
> > lh hemisphere, but it gives me the same result...
> >
> > Thanks for the link!
> >
> > Best,
> >
> > Loïc
> >
> > Le lun. 27 mai 2019 à 11:20, Tim Schäfer  a écrit :
> >   External Email - Use Caution
> >
> >   Hi Loïc,
> >
> >   that does not look correct, the data is definitely off. I'm not
> sure where
> >   the variables `mean_rest` and `surf.b` come from in your code, and
> I suspect
> >   that something is wrong with them.
> >
> >