External Email - Use Caution
From: freesurfer-request@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Date: Mon, 08 Jul 2019 11:34:24 -0400
Subject: Freesurfer Digest, Vol 185, Issue 11
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Skull Strip (Bruce Fischl)
2. How to Divide the Surface Parcellations of the Brain
(Mahshid Fouladivanda)
3. Re: How to Divide the Surface Parcellations of the Brain
(Bruce Fischl)
4. Assigning voxels different intensity values (Fotiadis, Panagiotis)
5. Re: Assigning voxels different intensity values (Bruce Fischl)
6. Re: Assigning voxels different intensity values
(Fotiadis, Panagiotis)
7. Re: Assigning voxels different intensity values (Bruce Fischl)
8. Re: Assigning voxels different intensity values
(Fotiadis, Panagiotis)
9. how to map regional t values on surface (fengmei fan)
10. Skull Strip (Admin)
11. Error in analyze (Qdec) (Abby tang)
12. Re: Freesurfer Digest, Vol 185, Issue 9 (vittal korann)
13. Postdoctoral Position opening at the University of Pittsburgh
in neuroimaging of mood disorders (Anna Manelis)
14. Re: make_average_subject error: could not load norm volume
from (null) (Greve, Douglas N.,Ph.D.)
15. Re: Skull Strip (Hoopes, Andrew)
16. Re: recon-all error: Correcting defect (Diamond, Bram Ryder)
17. Re: recon-all error: Correcting defect
(Miguel ?ngel Rivas Fern?ndez)
----------------------------------------------------------------------
Message: 1
Date: Sun, 7 Jul 2019 13:33:35 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Skull Strip
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907071333050.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
I believe I already answered this. I don't understand what amplified
noise you mean. The brainmask.mgz can be used with mri_mask to apply to
any input volume you want.
cheers
Bruce
On Sun, 7 Jul 2019, Admin wrote:
>
> ????????External Email - Use Caution????????
>
> Dear Freesurfer group? Now,I want ?generated a brain mask including the brain but excluding the
> amplified noise regions after skull strip, but I can't find the corresponding command line, so I
> send this email to you,?hoping to get your help.?
> My English is poor, if?I make mistakes ,?I hope you can understand me. Thanks for your help?
>
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Sincerely: Meng Nan Lin
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Date: 07/04/2019
>
>
>
>
> ?
>
>
>
>
> ?
>
>
>
------------------------------
Message: 2
Date: Mon, 08 Jul 2019 01:06:44 +0430
From: "Mahshid Fouladivanda" <M.Fouladivanda@sutech.ac.ir>
Subject: [Freesurfer] How to Divide the Surface Parcellations of the
Brain
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <WC20190707203644.661057@sutech.ac.ir>
Content-Type: text/plain; charset="us-ascii"
External Email - Use Caution
Dear Freesurfer Experts,
I would like to divide the surface parcellations of the neonatal brain. The
parcells were extracted using Draw_EM (Developing brain Region Annotation
With Expectation-Maximization), an atlas based segmentation, from cortical
and sub-cortical. As I understand from help comments,
mris_divide_parcellation would help, but it needs annotation file to be
imported as input. I do not have the annotation file. I would appreciate it
if you could help me how to divide my parcells in more regions?
Regards,
Mahshid
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/24c57303/attachment-0001.html
------------------------------
Message: 3
Date: Sun, 7 Jul 2019 18:27:49 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to Divide the Surface Parcellations of
the Brain
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907071827020.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"
Hi Mahshid
what format do you have? Can you convert to annot? Should be easy enough to
do in matlab using write_annotation.m
cheers
Bruce
On Mon, 8 Jul 2019,
Mahshid Fouladivanda wrote:
>
> ????????External Email - Use Caution????????
>
> Dear Freesurfer Experts,
> ?
> I would like to divide the surface parcellations?of the neonatal brain. The parcells were extracted
> using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an?atlas based
> segmentation,?from cortical and sub-cortical. As I understand from help comments,
> mris_divide_parcellation would help, but it needs annotation file?to be imported as input. I do not
> have the annotation file. I would appreciate it if you could help me how to divide my parcells in
> more regions?
> ?
> Regards,
> Mahshid
>
>
------------------------------
Message: 4
Date: Sun, 7 Jul 2019 23:16:23 +0000
From: "Fotiadis, Panagiotis" <PFOTIADIS@mgh.harvard.edu>
Subject: [Freesurfer] Assigning voxels different intensity values
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3AE32B6F-1B23-48F3-AEC9-A19C5B6CD629@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hello,
I was wondering whether there is a way to assign a different intensity value on each voxel within a parcellation file (such as aseg.mgz). What I?m essentially trying to do is create a file (using the aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do that in Freeview for each individual voxel but I wasn?t sure whether there was a more efficient/automated way in either bash or matlab.
Let me know if the above doesn?t make any sense, and thanks in advance!
Best,
Panos
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190707/7530dbf9/attachment-0001.html
------------------------------
Message: 5
Date: Sun, 7 Jul 2019 21:28:56 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Assigning voxels different intensity values
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907072128330.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Panos
I'm not sure I understand. Isn't that already what the aseg is? E.g.
voxel intensity 17 means left hippocampus?
Bruce
On Sun, 7 Jul 2019, Fotiadis,
Panagiotis wrote:
>
> Hello,
>
> ?
>
> I was wondering whether there is a way to assign a different intensity value on each voxel within a
> parcellation file (such as aseg.mgz). What I?m essentially trying to do is create a file (using the
> aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do
> that in Freeview for each individual voxel but I wasn?t sure whether there was a more
> efficient/automated way in either bash or matlab.
>
> Let me know if the above doesn?t make any sense, and thanks in advance!
>
> ?
>
> Best,
>
> Panos
>
> ?
>
>
>
------------------------------
Message: 6
Date: Mon, 8 Jul 2019 01:41:36 +0000
From: "Fotiadis, Panagiotis" <PFOTIADIS@mgh.harvard.edu>
Subject: Re: [Freesurfer] Assigning voxels different intensity values
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1FB3831F-5400-4947-A9ED-7754FFDCC4F3@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Bruce,
Thanks for your response! Within aseg, however, there is a group of voxels with intensity 17 (and therefore comprising the left hippocampus). I was mainly wondering whether there is a way to assign a different intensity value to each individual voxel in aseg (so that for instance if you had 40,000 voxels in aseg.mgz then you would assign each one with a different intensity value so that you would end up with 40,000 "ROIs" ).
Hope this clarifies a little bit my semi-abstract question!
Thanks again,
Panos
?On 7/7/19, 9:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Panos
I'm not sure I understand. Isn't that already what the aseg is? E.g.
voxel intensity 17 means left hippocampus?
Bruce
On Sun, 7 Jul 2019, Fotiadis,
Panagiotis wrote:
>
> Hello,
>
>
>
> I was wondering whether there is a way to assign a different intensity value on each voxel within a
> parcellation file (such as aseg.mgz). What I?m essentially trying to do is create a file (using the
> aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do
> that in Freeview for each individual voxel but I wasn?t sure whether there was a more
> efficient/automated way in either bash or matlab.
>
> Let me know if the above doesn?t make any sense, and thanks in advance!
>
>
>
> Best,
>
> Panos
>
>
>
>
>
------------------------------
Message: 7
Date: Sun, 7 Jul 2019 22:17:22 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Assigning voxels different intensity values
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1907072216070.916@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
oh, I see. It would be pretty easy to do in matlab. Something like:
v = load_mgh('aseg.mgz');
vnew = zeros(size(v))
left_hippo_ind = find(v == 17);
for i=1:length(left_hippo_ind)
vnew(i) = i
end
On Mon, 8 Jul 2019,
Fotiadis, Panagiotis wrote:
> Hi Bruce,
>
> Thanks for your response! Within aseg, however, there is a group of voxels with intensity 17 (and therefore comprising the left hippocampus). I was mainly wondering whether there is a way to assign a different intensity value to each individual voxel in aseg (so that for instance if you had 40,000 voxels in aseg.mgz then you would assign each one with a different intensity value so that you would end up with 40,000 "ROIs" ).
> Hope this clarifies a little bit my semi-abstract question!
>
> Thanks again,
> Panos
>
> ?On 7/7/19, 9:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
>
> Hi Panos
>
> I'm not sure I understand. Isn't that already what the aseg is? E.g.
> voxel intensity 17 means left hippocampus?
>
> Bruce
> On Sun, 7 Jul 2019, Fotiadis,
> Panagiotis wrote:
>
> >
> > Hello,
> >
> >
> >
> > I was wondering whether there is a way to assign a different intensity value on each voxel within a
> > parcellation file (such as aseg.mgz). What I?m essentially trying to do is create a file (using the
> > aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do
> > that in Freeview for each individual voxel but I wasn?t sure whether there was a more
> > efficient/automated way in either bash or matlab.
> >
> > Let me know if the above doesn?t make any sense, and thanks in advance!
> >
> >
> >
> > Best,
> >
> > Panos
> >
> >
> >
> >
> >
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 8
Date: Mon, 8 Jul 2019 02:49:31 +0000
From: "Fotiadis, Panagiotis" <PFOTIADIS@mgh.harvard.edu>
Subject: Re: [Freesurfer] Assigning voxels different intensity values
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <00D2E4AD-01ED-4FFD-B0C2-F4FD05E202B2@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Bruce,
That?s exactly what I needed, thank you!
Best,
Panos
?On 7/7/19, 10:18 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
oh, I see. It would be pretty easy to do in matlab. Something like:
v = load_mgh('aseg.mgz');
vnew = zeros(size(v))
left_hippo_ind = find(v == 17);
for i=1:length(left_hippo_ind)
vnew(i) = i
end
On Mon, 8 Jul 2019,
Fotiadis, Panagiotis wrote:
> Hi Bruce,
>
> Thanks for your response! Within aseg, however, there is a group of voxels with intensity 17 (and therefore comprising the left hippocampus). I was mainly wondering whether there is a way to assign a different intensity value to each individual voxel in aseg (so that for instance if you had 40,000 voxels in aseg.mgz then you would assign each one with a different intensity value so that you would end up with 40,000 "ROIs" ).
> Hope this clarifies a little bit my semi-abstract question!
>
> Thanks again,
> Panos
>
> On 7/7/19, 9:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
>
> Hi Panos
>
> I'm not sure I understand. Isn't that already what the aseg is? E.g.
> voxel intensity 17 means left hippocampus?
>
> Bruce
> On Sun, 7 Jul 2019, Fotiadis,
> Panagiotis wrote:
>
> >
> > Hello,
> >
> >
> >
> > I was wondering whether there is a way to assign a different intensity value on each voxel within a
> > parcellation file (such as aseg.mgz). What I?m essentially trying to do is create a file (using the
> > aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do
> > that in Freeview for each individual voxel but I wasn?t sure whether there was a more
> > efficient/automated way in either bash or matlab.
> >
> > Let me know if the above doesn?t make any sense, and thanks in advance!
> >
> >
> >
> > Best,
> >
> > Panos
> >
> >
> >
> >
> >
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 9
Date: Mon, 8 Jul 2019 04:01:19 +0000
From: fengmei fan <fanfengmei@live.com>
Subject: [Freesurfer] how to map regional t values on surface
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MW2PR12MB244272B7A4E3C48A02AF6B6FA1F60@MW2PR12MB2442.namprd12.prod.outlook.com>
Content-Type: text/plain; charset="gb2312"
External Email - Use Caution
Dear all,
I have used the command to calculate mean thickness:
aparcstats2table ?subjectsfile ${subjects_list} ?parc aparc.a2009s ?hemi lh ?meas ${meas} ?tablefile aparc.a2009s.${meas}.lh.txt
aparcstats2table ?subjectsfile ${subjects_list} ?parc aparc.a2009s ?hemi rh ?meas ${meas} ?tablefile aparc.a2009s.${meas}.rh.txt
And when i have t/r values for each region (74 per hemisphere), how to map them on surface?
like this one with colorbar representing t/r values?
[cid:_Foxmail.1@e5e8b321-1060-adcd-7310-68f457c85a95]
Best,
Fengmei
________________________________
fanfengmei@live.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/a2082a86/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Catch(07-08-11-57-45).jpg
Type: image/jpeg
Size: 36278 bytes
Desc: Catch(07-08-11-57-45).jpg
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/a2082a86/attachment-0001.jpg
------------------------------
Message: 10
Date: Mon, 8 Jul 2019 14:06:28 +0800 (CST)
From: Admin <15140248156@163.com>
Subject: [Freesurfer] Skull Strip
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <25a8fb6.7dc8.16bd030d230.Coremail.15140248156@163.com>
Content-Type: text/plain; charset="gbk"
External Email - Use Caution
Dear Freesurfer group?
just tried recon-all with the -use-gpu flag from the current development version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install(8.0). Does Freesurfer only work with cuda 5.0?
Date: 07/08/2019
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/f13dc62a/attachment-0001.html
------------------------------
Message: 11
Date: Mon, 8 Jul 2019 15:08:55 +0800
From: Abby tang <abbytang0925@gmail.com>
Subject: [Freesurfer] Error in analyze (Qdec)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAMuu6y+KxnuVW3VuWTqNqJKi8tHdPxtX7iUYrcy2evrjzRzN-A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello FreeSurfer Developers,
I want to compare the relationship between age and thickness, which is
controlled the effect about sex,education and eTIV, so QDEC was used.
However I met a problem when I use it, such as picture1.
I get the wrong message, Error in Analyze: command failed: mri_glmfit
--y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd
/home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir
/home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label
/home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat.
So I tried to put those to terminal, the feedback is:
gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 age 80.3537 2.43637
1 education 12.189 3.6099
2 eTIV 1.33934e+06 242446
Class Means of each Continuous Variable
1 sexFemale 80.0568 11.4773 1265564.4638
2 sexMale 80.6974 13.0132 1424768.7681
INFO: gd2mtx_method is dods
Reading source surface
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.984375
AvgVtxArea 0.399269
AvgVtxDist 0.721953
StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /home/abby/Desktop/qdecyoung/qdec
cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh
--fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir
/home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label
/home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux
hostname abby-virtual-machine
machine x86_64
user abby
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh
logyflag 0
usedti 0
FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd
labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled
Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh
... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat
Computing normalized matrix
Normalized matrix condition is 9294.65
Matrix condition is 1e+08
Found 148151 points in label.
Pruning voxels by thr: 1.175494e-38
Found 139197 voxels in mask
Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh
Reshaping mriglm->mask...
search space = 69257.619818
DOF = 156
Starting fit and test
Fit completed in 0.338183 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391
Writing results
lh-Avg-Intercept-thickness
maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975
MatrixMultiplyD(): m2 is null
break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally.
I don't know why. Please help me. Thank you
Best regards
abby
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/622ebec7/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: f088d7774c8cb3963df7058b319ac44.png
Type: image/png
Size: 164359 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/622ebec7/attachment-0001.png
------------------------------
Message: 12
Date: Mon, 8 Jul 2019 16:13:49 +0530
From: vittal korann <vittalkorann@gmail.com>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 9
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACyMoT2dEJAfQCYQn4mSPL=EQ1pVPGtGw_+1nBJa2qFjmA=+dA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thanks, Tim for your reply.
No, there is only "lh.pial" file exists not 'lh.pial_lgi.
What might be the problem?
Any help would be appreciated
Thanks & regards
-Korann
On Sat, Jul 6, 2019 at 9:30 PM <freesurfer-request@nmr.mgh.harvard.edu>
wrote:
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-request@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-owner@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. Re: [External] Re: rostral anterior cingulate fix?
> (Zeng,Victor (BIDMC - Psychiatry))
> 2. Re: [External] Re: rostral anterior cingulate fix? (Bruce Fischl)
> 3. Re: recon-all Error : inputs cannot have multiple frames.
> ( Yueming )
> 4. Re: recon-all Error : inputs cannot have multiple frames.
> (Bruce Fischl)
> 5. error while running pial_lgi for gyrification index
> (vittal korann)
> 6. Re: error while running pial_lgi for gyrification index
> (Tim Sch?fer)
> 7. Viewing Uncorrected Significance Map in Freeview (Marie Hill)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 5 Jul 2019 17:42:28 +0000
> From: "Zeng,Victor (BIDMC - Psychiatry)" <vzeng@bidmc.harvard.edu>
> Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate
> fix?
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <1562348548910.95994@bidmc.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Sorry, I thought I attached something
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> ph: 617 754 1237
> --
>
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <
> fischl@nmr.mgh.harvard.edu>
> Sent: Friday, July 5, 2019 10:24 AM
> To: Freesurfer support list
> Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
>
> Hi Victor
>
> can you render the parcellation in that area on the surface (in freeview)
> and show it to us?
>
> cheers
> Bruce
>
>
> On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
>
> >
> > Hi Freesurfer group -
> >
> >
> > I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm
> seeing a misparcellation of
> > the right rostral anterior cingulate using tkmedit (I know tkmedit is
> sorta deprecated), and it
> > doesn't seem inappropriate to use control point fixes. How would you
> best fix this (I'm open to
> > using freeview), without just editing the aparc+aseg.mgz?
> >
> >
> > Victor Zeng
> > Beth Israel Deaconess Medical Center
> > Keshavan Lab
> > ph: 617 754 1237
> > --
> >
> >
> ____________________________________________________________________________________________________
> >
> > This message is intended for the use of the person(s) to whom it may be
> addressed. It may contain
> > information that is privileged, confidential, or otherwise protected
> from disclosure under
> > applicable law. If you are not the intended recipient, any
> dissemination, distribution, copying, or
> > use of this information is prohibited. If you have received this message
> in error, please
> > permanently delete it and immediately notify the sender. Thank you.
> >
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Screenshot from 2019-07-05 13-41-46.png
> Type: image/png
> Size: 41889 bytes
> Desc: Screenshot from 2019-07-05 13-41-46.png
> Url :
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190705/626cd039/attachment-0001.png
>
> ------------------------------
>
> Message: 2
> Date: Fri, 5 Jul 2019 13:45:40 -0400 (EDT)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate
> fix?
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <alpine.LRH.2.20.1907051345020.916@door.nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> you did, but not a surface rendering. Load it with freeview and show it as
> a surface (maybe inflated and white)
>
> On Fri, 5 Jul 2019, Zeng,Victor (BIDMC
> - Psychiatry) wrote:
>
> >
> > Sorry, I thought I attached something
> > Victor Zeng
> > Beth Israel Deaconess Medical Center
> > Keshavan Lab
> > ph: 617 754 1237
> > --
> >
> > ________________________________________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <
> fischl@nmr.mgh.harvard.edu>
> > Sent: Friday, July 5, 2019 10:24 AM
> > To: Freesurfer support list
> > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix?
> >
> > Hi Victor
> >
> > can you render the parcellation in that area on the surface (in freeview)
> > and show it to us?
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
> >
> >>
> >> Hi Freesurfer group -
> >>
> >>
> >> I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm
> seeing a misparcellation of
> >> the right rostral anterior cingulate using tkmedit (I know tkmedit is
> sorta deprecated), and it
> >> doesn't seem inappropriate to use control point fixes. How would you
> best fix this (I'm open to
> >> using freeview), without just editing the aparc+aseg.mgz?
> >>
> >>
> >> Victor Zeng
> >> Beth Israel Deaconess Medical Center
> >> Keshavan Lab
> >> ph: 617 754 1237
> >> --
> >>
> >>
> ____________________________________________________________________________________________________
> >>
> >> This message is intended for the use of the person(s) to whom it may be
> addressed. It may contain
> >> information that is privileged, confidential, or otherwise protected
> from disclosure under
> >> applicable law. If you are not the intended recipient, any
> dissemination, distribution, copying, or
> >> use of this information is prohibited. If you have received this
> message in error, please
> >> permanently delete it and immediately notify the sender. Thank you.
> >>
> >>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 6 Jul 2019 10:36:28 +0800
> From: " Yueming " <1028551592@qq.com>
> Subject: Re: [Freesurfer] recon-all Error : inputs cannot have
> multiple frames.
> To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <tencent_1282426509F1FBABD7C044C444A589BB2209@qq.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> External Email - Use Caution
>
> My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p
> I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple?
> My inputs' format is dicom,when it is about 200kB,the software can run and
> has no such error.but when the dicom is more than 500kB,the next error will
> happen:
>
>
>
>
> Checking for (invalid) multi-frame inputs...
> ERROR: input(s) cannot have multiple frames!
> /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames
>
>
>
> My English is so bad that you know...... Forgive me,please!
>
>
> WISH TO YOUR TEACHING AND REPLY.
>
> >From a graduate student of China Liaoning University .
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/560e6132/attachment-0001.html
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: not available
> Type: image/jpeg
> Size: 14156 bytes
> Desc: not available
> Url :
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/560e6132/attachment-0001.jpe
>
> ------------------------------
>
> Message: 4
> Date: Fri, 5 Jul 2019 22:42:30 -0400 (EDT)
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all Error : inputs cannot have
> multiple frames.
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <alpine.LRH.2.20.1907052241330.916@door.nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I think the dicom series that 1.DCM is part of is not a 3D T1-weighted
> structural. Can you run mri_info on it, or dcmdump (or both)?
> On Sat, 6 Jul
> 2019, Yueming wrote:
>
> >
> > ????????External Email - Use Caution????????
> >
> > My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p?
> > I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple?
> > My inputs' format is dicom,when it is about 200kB,the software can run
> and has no such error.but
> > when the dicom is more than 500kB,the next error will happen:
> >
> > [IMAGE]
> > Checking for (invalid) multi-frame inputs...
> > ERROR: input(s) cannot have multiple frames!
> > /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames
> >
> > My English is so bad that you know......? Forgive me,please!
> >
> > WISH TO YOUR TEACHING AND REPLY.
> > From a graduate student?of China Liaoning University .?
> >
> >
>
> ------------------------------
>
> Message: 5
> Date: Sat, 6 Jul 2019 16:57:28 +0530
> From: vittal korann <vittalkorann@gmail.com>
> Subject: [Freesurfer] error while running pial_lgi for gyrification
> index
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <
> CACyMoT1CW-wS37dHyamo1WTf4NP-V1Ov0MMY6mjEaVtk3pV-uA@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hi FS experts,
>
> I wanted to run the gyrification index for all patients with Schizophrenia
> and volunteers. When I entered the command:
> "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output
>
> " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> Actual FREESURFER_HOME /usr/local/freesurfer
> -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02
> /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> '/usr/local/freesurfer/bin/recon-all' ->
> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy'
> #--------------------------------------------
> #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019
> /usr/local/freesurfer/subjects/SATM124/surf
>
> mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage
> --out lh.pial_lgi.fsaverage.mgh
>
> nsubjects = 1
> ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi
> Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019
>
> For more details, see the log file
> /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
>
> I never faced this problem before while running gyrification index. To me,
> it's looks bizarre.
> Would appreciate any help.
>
> Thanks & regards
> -Korann
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/684397d5/attachment-0001.html
>
> ------------------------------
>
> Message: 6
> Date: Sat, 6 Jul 2019 14:02:03 +0200 (CEST)
> From: Tim Sch?fer <ts+ml@rcmd.org>
> Subject: Re: [Freesurfer] error while running pial_lgi for
> gyrification index
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <1748678951.441799.1562414523805@ox.hosteurope.de>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Just to be sure: *does*
> /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi exist?
>
> Tim
>
> > On July 6, 2019 at 1:27 PM vittal korann <vittalkorann@gmail.com> wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hi FS experts,
> >
> > I wanted to run the gyrification index for all patients with
> Schizophrenia
> > and volunteers. When I entered the command:
> > "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal
> output
> >
> > " Subject Stamp:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > Actual FREESURFER_HOME /usr/local/freesurfer
> > -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02
> > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6
> 12:03:31
> > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> > '/usr/local/freesurfer/bin/recon-all' ->
> > '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy'
> > #--------------------------------------------
> > #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019
> > /usr/local/freesurfer/subjects/SATM124/surf
> >
> > mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage
> > --out lh.pial_lgi.fsaverage.mgh
> >
> > nsubjects = 1
> > ERROR: cannot find
> /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi
> > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6
> 12:03:31
> > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019
> >
> > For more details, see the log file
> > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log
> > To report a problem, see
> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"
> >
> > I never faced this problem before while running gyrification index. To
> me,
> > it's looks bizarre.
> > Would appreciate any help.
> >
> > Thanks & regards
> > -Korann
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Dr. Tim Sch?fer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sat, 6 Jul 2019 13:38:54 +0000
> From: Marie Hill <marie_hill@outlook.com>
> Subject: [Freesurfer] Viewing Uncorrected Significance Map in Freeview
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <
> LNXP123MB1817D23EE50CB4F16728A2E0F0F40@LNXP123MB1817.GBRP123.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> External Email - Use Caution
>
> Hi everyone,
>
>
> I have just finished running glmfit. When I try to load the significance
> maps in freeview, they appear to load for a moment and then disappear, just
> showing the brain volume without any highlighted areas of significance.
> Does anyone have any idea why this could be?
>
>
> I ran the command: freeview -f
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
>
> Kindest Regards,
>
>
> Marie
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/15f4b7fd/attachment-0001.html
>
> ------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 185, Issue 9
> ******************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/a5d5dd87/attachment-0001.html
------------------------------
Message: 13
Date: Mon, 8 Jul 2019 10:05:35 -0400
From: Anna Manelis <anna.manelis@gmail.com>
Subject: [Freesurfer] Postdoctoral Position opening at the University
of Pittsburgh in neuroimaging of mood disorders
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAN+AquJFHyNoq+VAzT-WsMW5JonGaBf8UCf-s0=Paey_bmEwDw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Candidates are being considered for a post-doctoral associate position in
the Anticipation, Cognition and Emotion lab ( www.ace.pitt.edu ) at the
University of Pittsburgh (http://www.pitt.edu) to work with Dr. Anna
Manelis and her team. A successful candidate will work on the NIMH funded
research project that uses multimodal neuroimaging (fMRI, MRI, DTI and
fNIRS) to understand the contribution of anticipatory processing to
cognitive and emotional dysfunction in individuals with mood disorders.
Pittsburgh is a vibrant community which promotes diversity and
collaboration within its university and medical systems. Our lab works in
conjunction with the University of Pittsburgh Medical Center to perform
neuroimaging studies which will help us to better understand mood
disorders, including major depressive disorder and bipolar disorders.
*Required Qualification*s: we are seeking a highly motivated candidate with
a PhD degree (or anticipated PhD degree) in psychology, cognitive
neuroscience, computational neuroscience or a related discipline. A strong
research background in the analysis and interpretation of neuroimaging data
is required. A successful candidate will have excellent writing and
communication skills. Candidates with a strong computational background are
encouraged to apply. Experience with FSL, Freesurfer and E-prime is
preferred. The ability to program in Shell, Matlab, Python and/or R is
preferred. Experience with fNIRS, graph modeling and pattern
classification analyses is a plus. While prior experience with clinical
populations is not necessary, we expect candidates to be interested in
neuroimaging research of working and episodic memory and/or anticipatory
and emotional processing in individuals with mood disorders.
*Responsibilities*:
? Help to run fMRI/fNIRS experiments
? Analyze fMRI, MRI, DTI and fNIRS neuroimaging data
? Write manuscripts
? Present findings from studies at conferences
This is a full-time position that can be extended to 3 years. We are
looking for someone to join our lab in Fall 2019 (with some flexibility).
This position is funded by the NIMH and salary will vary based on
experience.
If you are interested in this position, please send a CV, research
statement, preprints/reprints of papers, and the names and contact
information for two references to *Anna Manelis (manelisa@upmc.edu
<manelisa@upmc.edu>).*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/b124dce3/attachment-0001.html
------------------------------
Message: 14
Date: Mon, 8 Jul 2019 14:43:22 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject error: could not load
norm volume from (null)
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <8da547e7-2123-2a69-1524-bd45602936bb@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Can you send the full terminal output of make_average_subject? There should also be some log files (make_average_volume.log and make_average_surface.log) in the average subject that would be helpful
On 7/4/2019 4:36 AM, Mads Jensen wrote:
External Email - Use Caution
HI FreeSurfer Developers,
I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:
Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000 0.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 -128.00000;
0.00000 -1.00000 0.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
mghRead(mri/norm.mgz, -1): could not open file
-------------------------
Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)
Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux
I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/16baceec/attachment-0001.html
------------------------------
Message: 15
Date: Mon, 8 Jul 2019 15:05:15 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Skull Strip
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0670CFC5-D6B7-4C68-A5CC-68FFAB05DF28@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi, unless you build the binaries yourself, I believe the stable freesurfer versions only support cuda 5. However, cuda support has been completely removed in the current development version. The dev version that you?re referencing is from 2016.
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Admin <15140248156@163.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, July 8, 2019 at 2:07 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Skull Strip
External Email - Use Caution
Dear Freesurfer group?
just tried recon-all with the -use-gpu flag from the current development version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0), but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install(8.0). Does Freesurfer only work with cuda 5.0?
Date: 07/08/2019
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/415c2680/attachment-0001.html
------------------------------
Message: 16
Date: Mon, 8 Jul 2019 15:15:56 +0000
From: "Diamond, Bram Ryder" <BRDIAMOND@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all error: Correcting defect
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN8PR04MB5473C290BE1997823A50156CE2F60@BN8PR04MB5473.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Miguel!
I'll be happy to help with your issue, but I'm having trouble finding your subject's directory on our server. Could you please try and upload the data via FTP, again? Also, have you tried either of Bruce's suggestions?
Thanks,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel ?ngel Rivas Fern?ndez <miguelrivasfdez@gmail.com>
Sent: Wednesday, June 26, 2019 11:37 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution
Hello Bruce,
Ok, I have sent to you the subject via FileDrop if you want to take a look. Thanks.
Best regards,
El mi?., 26 jun. 2019 a las 17:04, Bruce Fischl (<fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>) escribi?:
Hi Miguel
depending on the lesions it may not be fixable (since they may change the
topology of the cortex). If you upload the subject we will take a look, or
you can try manually filling in the lesion in the wm.mgz (or marking it as
lesion in the aseg.mgz) and seeing if that helps
cheers
Bruce
On Wed, 26 Jun 2019, Miguel ?ngel Rivas
Fern?ndez wrote:
>
> External Email - Use Caution
>
>
> I ran the recon-all in one subject and and this process was stopped in the topology correction. In
> particular during the
>
> "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
>
> I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview and I noticed that the this
> error would be located in the lh.inflated.nofix file. I am not completely sure but I suspect that
> this error may be due to the fact that there is a large amount of brain lesion and this would
> difficult the topology correction. How can I fix this problem?
>
> Thanks in advance.
>
> Best regards,
>
> --
> Miguel ?ngel Rivas Fern?ndez
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Miguel ?ngel Rivas Fern?ndez
------------------------------
Message: 17
Date: Mon, 8 Jul 2019 17:34:08 +0200
From: Miguel ?ngel Rivas Fern?ndez <miguelrivasfdez@gmail.com>
Subject: Re: [Freesurfer] recon-all error: Correcting defect
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CALf-+QGnN0Y4E4S=HLoi89hdNuCB97TG=HjThf3OXd-_aJ_jqQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Bram,
Thanks for your help, yes I tried to fix this issue following Bruce?s
suggestions and everything worked fine. I manually filled the brain lesions
in the wm.mgz and now the recon-all did not stop in the correcting defect.
Best regards,
El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (<
BRDIAMOND@mgh.harvard.edu>) escribi?:
> Hi Miguel!
>
> I'll be happy to help with your issue, but I'm having trouble finding your
> subject's directory on our server. Could you please try and upload the data
> via FTP, again? Also, have you tried either of Bruce's suggestions?
>
> Thanks,
> Bram
>
> Bram R. Diamond, BSc
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel ?ngel Rivas
> Fern?ndez <miguelrivasfdez@gmail.com>
> Sent: Wednesday, June 26, 2019 11:37 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error: Correcting defect
>
> External Email - Use Caution
>
> Hello Bruce,
>
> Ok, I have sent to you the subject via FileDrop if you want to take a
> look. Thanks.
>
> Best regards,
>
> El mi?., 26 jun. 2019 a las 17:04, Bruce Fischl (<
> fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>) escribi?:
> Hi Miguel
>
> depending on the lesions it may not be fixable (since they may change the
> topology of the cortex). If you upload the subject we will take a look, or
> you can try manually filling in the lesion in the wm.mgz (or marking it as
> lesion in the aseg.mgz) and seeing if that helps
>
> cheers
> Bruce
> On Wed, 26 Jun 2019, Miguel ?ngel Rivas
> Fern?ndez wrote:
>
> >
> > External Email - Use Caution
> >
> >
> > I ran the recon-all in one subject and and this process was stopped in
> the topology correction. In
> > particular during the
> >
> > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
> >
> > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview
> and I noticed that the this
> > error would be located in the lh.inflated.nofix file. I am not
> completely sure but I suspect that
> > this error may be due to the fact that there is a large amount of brain
> lesion and this would
> > difficult the topology correction. How can I fix this problem?
> >
> > Thanks in advance.
> >
> > Best regards,
> >
> > --
> > Miguel ?ngel Rivas Fern?ndez
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Miguel ?ngel Rivas Fern?ndez
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
--
*Miguel ?ngel Rivas Fern?ndez*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190708/e9ad351b/attachment.html
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 185, Issue 11
*******************************************