[Freesurfer] area.pial files for fsaverage

[Xiaojiang Yang]

External Email - Use Caution

Dear FS developers,

I have noticed that for each subject, there are ?h.area and ?h.area.pial
files under the $SUBJECT_DIR/$subject/surf sub-directory. According to
Bruce's words from here
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23751.html,
they are for white surfaces and pial surfaces respectively. But for the
fsaverage subject, I only find file ?h.area; there are no ?h.area.pial
files existing. Could you tell me why? and where can I get those files?

Thanks!
Xiao
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Re: [Freesurfer] mri_fieldsign error

[Xiaomin Yue]

External Email - Use Caution

I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel  fedora’ with the 
same “segmentation fault (core dumped)” error.

Thanks,
Xiaomin

From: Xiaomin Yue
Sent: Friday, July 17, 2020 6:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_fieldsign error


External Email - Use Caution

Yes.  I will try it on a real Linux box and let you know.


Thanks,
Xiaomin

From: Douglas N. Greve
Sent: Friday, July 17, 2020 5:32 PM
To: Xiaomin Yue; Freesurfer support 
list
Subject: Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it has something 
to do with WSL. Do you have a real linux box you can try it on?
On 7/17/2020 5:24 PM, Xiaomin Yue wrote:

External Email - Use Caution
HI Doug,

Sorry for the slow response.  I got the same “segmentation fault (core dumped)” 
error when running the left hemi. I tested it multiple times.   Does this 
function create a detailed log I can send to you?

Thanks,
Xiaomin

From: Douglas N. Greve
Sent: Friday, July 17, 2020 1:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You sent me left hemi 
data, so I ran the command below

mri_fieldsign --fs fieldsign.71.nii.gz --polar LOO.wedge.polar.lh.real.nii.gz 
LOO.wedge.polar.lh.imag.nii.gz --eccen LOO.ring.eccen.lh.real.nii.gz 
LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere

But I also noticed that the command that you gave below is for the right hemi. 
Do you know if the left hemi works?


On 7/11/2020 1:43 PM, Xiaomin Yue wrote:

External Email - Use Caution
Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.  Since the ring and wedge 
were presented at a different frequency, the data had to be analyzed separately 
for each condition.  To get the field sign, I had to use the mri_fieldsign 
function to combine polar and eccen data.   However, an error happened with 
running mri_fieldsign: “Segmentation fault  (core dumped)”.  The following 
is the command-line output.

Thanks for your help!
Xiaomin


cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala
cmdline mri_fieldsign --fs 
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar 
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz 
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz 
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO 
--hemi rh --sphere
sysname  Linux
hostname DESKTOP-SVDQE4Q
machine  x86_64
user xiaominyue
eccen real  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
eccen imag  ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz
polar real  LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
polar imag  LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz
patch (null)
subject LOO
hemirh
fwhm-1.00
nsmooth -1
fieldsign   LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz
usenew  1
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere
Using spherical coordinates
Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
Rot (rad): 0 0
surfer: compute_fieldsign2()
dthresh = 1.5
shape = 1
nvertices = 153801
0 0 45452   0.03  33.2224
1018  1000 39160  21.33  -18.3959
2055  2000 44734  43.26  33.0783
3148  3000 49793  65.38  0.653687
4344  4000 38626  88.16  16.7555
5529  5000 54149 110.12  -4.90118
6706  6000 61599 133.36  -5.74607
7971  7000 50134 155.88  -17.5589
9165  8000 34182 178.05  -18.9387
10591  9000 59682 200.70  -4.60514
12034 1 63856 223.18  -4.4884
13297 11000 41007 245.62  27.3489
14938 12000 27365 267.70  -1.40077
16684 13000 23615 289.10  -0.518007
18048 14000 47088 309.37  18.7017
19798 15000 21060 330.11  15.9458
21681 16000 33067 350.27  -11.1953
23173 17000 28744 371.48  -6.18747
25112 18000 27738 392.41  -6.93845
26953 19000 20538 414.47  2.99349
28903 2 80583 435.98  -0.338512
30319 21000 16251 459.83  -45.2313
32174 22000 17139 483.36  -2.31642
34093 23000 13307 507.02  19.1461
36170 24000 17826 530.65  -10.7575
37683 25000 69324 555.78  -6.17011
39666 26000 14043 583.29  -10.5151
41746 27000 76017 609.92  -0.0112556
43986 28000 84646 636.28  1.24722
46088 29000 9763 664.26  12.7035
48326 3 92161 694.30  2.03416
50431 31000 99884 724.91  1.20525
./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault  (core 
dumped) mri_fieldsign --fs 

[Freesurfer] outlier detection and remove

[Zeng, Qi]

External Email - Use Caution

Hi,

I have a question about how to handle outliers in aparc, aseg and tracula
results? Usually, each subject has one result regarding one measurement and
I detect and remove outliers using barplot. However, for results in
freesurfer, we have multiple outcomes for each region in terms of
measurements of aparc, aseg and tracula. Do we detect outliers for specific
regions or tracts and remove the outliers? Or detect which subjects have
outliers consistently for all the regions, and then we remove the subjects?
Thank you so much !

Best,
Qi

-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] How to do permutation for multiple comparison correction?

[Xiaojiang Yang]

External Email - Use Caution

Hi Doug,


For your questions:


1. "Not sure what you mean by in the ROI. Are you trying to permute
across space? That generally does not work because the points are not
exchangeable across space."


By "In the ROI", I mean for all vertices listed in the label file.
Here, I am talking about a test subject and n control subjects, they
are all considered in the same reference subject space - fsaverage. A
ROI is defined by a label file for the subject fsaverage. So, I am
comparing the test subject and control group on the same ROI region,
vertex by vertex. I want to permute points in the test subject and
points in all subjects in control groups.


I am not talking about permuting vertex locations; I am talking about
permuting values (thickness in my case) from subjects on each vertex.
For example, for vertex i, I have one value (v0) from test subject,
and n values (v1, v2,...vn) from control subjects:


test subject  control subjects

v0v1, v2, .. vn


One way of permutation would be:

test subject  control subjects

v1v0, v2, .. vn


Is this a reasonable way to do permutation?

2. "Not sure. You cannot discriminate between the groups when you are
doing permutation"


By doing the permutation many (say 1000) times, I want to get the
probability distribution of the sampling (observed or test) data
inside the ROI area, so that I can decide if I should reject or accept
null hypothesis based on cluster-wise significance level. What
problems do you think I have in this idea?


Thanks a lot!


On 7/21/2020 1:12 AM, Xiaojiang Yang wrote:

External Email - Use Caution

Dear FS experts,


Instead of using mri_glmfit-sim, I am trying to implement a customized multiple
comparison correction algorithm using permutation. Before I implement my
own, I want to make sure my permutation idea is correct. So I was looking
at how mri_glmfit-sim does the permutation. The link here
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has a
simple description for how to do permutation, but I don't quite understand
the 1st step: Permute the design matrix. To me, permute the design matrix
means permute the matrix rows here, but still hard to understand why
permuting matrix rows does the trick.

This is pretty standard in permutation. I think Tom Nichols has some basic
tutorials on how permutations work.

Anyway, I will not use any design matrix in my customized implementation,
so it does not matter for now. My problem can be described as follows: if I
have a ROI (a label file) on fsaverage, and I have a test subject and a
group of control subjects whose thickness values on every vertex in this
label are all known. (The test subject and control subjects are all using
fsaverage reference space). I want to compare this test subject's
thickness within
the ROI to a control group of subjects (within the same ROI). This is a
multiple-comparison problem, so I want to use permutation to get less FP
rate. My question is: How do I permute the test subject's points and
control subjects' points in ROI?

Not sure what you mean by in the ROI. Are you trying to permute across space?
That generally does not work because the points are not exchangeable across
space.

My understanding is that: for each point in the label, I randomly re-assign
all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is
the number of subjects in control group). And when all points in the label
are done, this is only 1 permutation. I will need at least 1000 times of
permutation to get the comparison statistics.

Is my understanding right?

Not sure. You cannot discriminate between the groups when you are doing
permutation

Thank you!
Xiao
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Re: [Freesurfer] PETSurfer questions - Part II

[Douglas N. Greve]

On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Many thanks for the reply,

Yep, unfortunately MG values are always much higher than SGTM ones (in 
all the ROIs).
I wonder whether this might be related (for MG and MZ) to the absence 
of a normalization using the pons as a reference.


Indeed, when I look at the file with mean values extracted for each 
modality, I see that the pons has always 1000 as mean uptake value for 
no PVC and SGTM, while for MG and MZ values in the pons range from 
-0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you 
using? In version 6, pons was considered white matter, but I changed it 
to gray matter in version 7. The bottom line on this is that you cannot 
compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then 
its value is bogus.


Below are the commands I’ve used to obtain the MG and MZ values:

1) With Muller-Gartner (MG):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output


 Then:

mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum 
MG_ROI.txt


2) With Meltzer (MZ):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o 
gtm_MZ.output


Then:

mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
MZ_ROI.txt



Do you recognize any errors in the commands?


Many thanks,

Pilar







Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" >

Subject: Re: [Freesurfer] PETSurfer analysis question
To: >
Message-ID: >

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


The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?


On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar









Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu 


 ha scritto:

Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:


External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull 

Re: [Freesurfer] Fwd: Cortical Parcellations in FreeDurger 7

[Douglas N. Greve]

I don't know. I'm not that familiar with FSL programs. If you want our 
help, try using mri_segstats. If something goes wrong send the command line


On 7/21/2020 10:26 AM, Al Qadi, Ameen wrote:


External Email - Use Caution

Hi Douglas,

I see the CLUT file, it's the same one I've been using. I have been 
using FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg 
using the CLUT indices as thresholds. This normally works, but results 
in empty ROIs for thalamic nuclei (but not for whole thalamus). What 
do you think could be the problem?


Best,
Ameen

On Fri, Jul 17, 2020 at 10:33 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:




On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:


External Email - Use Caution

Dear Freesurfer Developers,


I hope this email finds you all safe and well. I have two
questions regarding the new version of freesurfer:

  * Is there a new CLUT associated with FS7? I tried to use the
CLUT labels to extract thalamic subnuclei ROIs, but got empty
ROI files.


They should be  in $FREESURFER/FreeSurferColorLUT.txt
How are you extracting?


  * Given that Freesurfer version 7 contains segmentations not
previously generated in recon-all (i.e. hippocampal
subfields), is it possible to extract these ROIs using
aparc+aseg images generated using previous versions of
Freesurfer? Or do we need to repeat the cortical
parcellations (i.e. rerun recon-all) using FS7?


You can run  the hippocamal and thalamic segs on FS version 6
subjects.


I’d highly appreciate your time and feedback on this matter.
Thank you.


Best,

Ameen

-- 
Ameen Al Qadi

MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu 

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--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu 
--
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu 


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Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects

[Douglas N. Greve]

This is a known problem with mri_cc on Mac. Any day now we will release 
7.1.1 that will include a patch to fix this.


On 7/21/2020 7:05 AM, Annelies Vant Westeinde wrote:


External Email - Use Caution

Hi, I am attaching some recon-all log files as requested (hope it 
works like that).


Thanks!

Annelies van't Westeinde | PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskavägen 37A
+46 760967499
annelies.vant.westei...@ki.se | ki.se 
__
Karolinska Institutet – a medical university

*From:* Annelies Vant Westeinde
*Sent:* 15 July 2020 16:52
*To:* Freesurfer support list 
*Subject:* recon all Freesurfer 7.1 on Mac High Sierra fails to run 
for some subjects

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on 
a Mac operating system seems to fail for around 10% of the subjects.


The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
  -o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of 
them at the following step:


"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.


Annelies

Annelies van't Westeinde | PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskavägen 37A
+46 760967499
annelies.vant.westei...@ki.se | ki.se 
__
Karolinska Institutet – a medical university



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Re: [Freesurfer] How to do permutation for multiple comparison correction?

[Douglas N. Greve]

On 7/21/2020 1:12 AM, Xiaojiang Yang wrote:


External Email - Use Caution

Dear FS experts,

Instead of using mri_glmfit-sim, I am trying to implement a customized 
multiple comparison correction algorithm using permutation. Before I 
implement my own, I want to make sure my permutation idea is correct. 
So I was looking at how mri_glmfit-sim does the permutation.
The link here 
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has 
a simple description for how to do permutation, but I don't quite 
understand the 1st step: Permute the design matrix. To me, permute the 
design matrix means permute the matrix rows here, but still hard to 
understand why permuting matrix rows does the trick.
This is pretty standard in permutation. I think Tom Nichols has some 
basic tutorials on how permutations work.
Anyway, I will not use any design matrix in my customized 
implementation, so it does not matter for now.
My problem can be described as follows: if I have a ROI (a label file) 
on fsaverage, and I have a test subject and a group of control 
subjects whose thickness values on every vertex in this label are all 
known. (The test subject and control subjects are all using fsaverage 
reference space). I want to compare this test subject's thickness 
within the ROI to a control group of subjects (within the same ROI). 
This is a multiple-comparison problem, so I want to use permutation to 
get less FP rate.
My question is: How do I permute the test subject's points and control 
subjects' points in ROI?
Not sure what you mean by in the ROI. Are you trying to permute across 
space? That generally does not work because the points are not 
exchangeable across space.
My understanding is that: for each point in the label, I randomly 
re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects 
(where n is the number of subjects in control group). And when all 
points in the label are done, this is only 1 permutation. I will need 
at least 1000 times of permutation to get the comparison statistics.

Is my understanding right?
Not sure. You cannot discriminate between the groups when you are doing 
permutation

Thank you!
Xiao


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[Freesurfer] Fwd: Cortical Parcellations in FreeDurger 7

[Al Qadi, Ameen]

External Email - Use Caution

Hi Douglas,

I see the CLUT file, it's the same one I've been using. I have been using
FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the
CLUT indices as thresholds. This normally works, but results in empty ROIs
for thalamic nuclei (but not for whole thalamus). What do you think could
be the problem?

Best,
Ameen

On Fri, Jul 17, 2020 at 10:33 AM Douglas N. Greve 
wrote:

>
>
> On 7/17/2020 10:25 AM, Al Qadi, Ameen wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Developers,
>
>
> I hope this email finds you all safe and well. I have two questions
> regarding the new version of freesurfer:
>
>- Is there a new CLUT associated with FS7? I tried to use the CLUT
>labels to extract thalamic subnuclei ROIs, but got empty ROI files.
>
> They should be  in $FREESURFER/FreeSurferColorLUT.txt
> How are you extracting?
>
>
>- Given that Freesurfer version 7 contains segmentations not
>previously generated in recon-all (i.e. hippocampal subfields), is it
>possible to extract these ROIs using aparc+aseg images generated using
>previous versions of Freesurfer? Or do we need to repeat the cortical
>parcellations (i.e. rerun recon-all) using FS7?
>
> You can run  the hippocamal and thalamic segs on FS version 6 subjects.
>
> I’d highly appreciate your time and feedback on this matter. Thank you.
>
>
> Best,
>
> Ameen
> --
> Ameen Al Qadi
> MSBS Candidate
> Icahn School Of Medicine at Mount Sinai '20
> +1-646-500-1521
> ameen.alq...@icahn.mssm.edu
>
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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-- 
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
-- 
Ameen Al Qadi
MSBS Candidate
Icahn School Of Medicine at Mount Sinai '20
+1-646-500-1521
ameen.alq...@icahn.mssm.edu
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Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

[Douglas N. Greve]

Yep, I just found that error yesterday. I put a new longmc script in 
that same location with another fix -- but I have not fully tested it yet:)


On 7/21/2020 1:12 AM, Knut J Bjuland wrote:


External Email - Use Caution

Thanks it worked for subjects with more than one timepoint but when I 
ran on subjects with one timepoint I get this error? I can upload this 
subjects.



 mri_robust_template --mov 
/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz 
/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz --ixforms 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002.lta 
--average 1 --noit --template 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz 
--iscalein 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001-iscale.txt 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/002-iscale.txt 



7.1.0

--mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz as 
movable/source volume.
--mov: Using /cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz as 
movable/source volume.

    Total: 2 input volumes
--ixforms: Will use init XFORMS.
--average: Using method 1 for template computation.
--noit: Will output only first template (no iterations)!
--template: Using 
/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/rawavg.mgz 
as template output volume.

--iscalein: Will use init intensity scales
reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz'...
converting source 
'/cluster/work/jobs/1011199/KG01_Run1/mri/orig/001.mgz' to bspline ...

MRItoBSpline degree 3
reading source '/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz'...
converting source 
'/cluster/work/jobs/1011199/KG01_Run1/mri/orig/002.mgz' to bspline ...

MRItoBSpline degree 3
error: No such file or directory
error: 
ltaReadFile(/cluster/work/jobs/1011199/KG01_Run1.long.KG01_Run1_base/mri/orig/001.lta): 
can't open file^@

Segmentation fault (core dumped)
ERROR:
@#@FSTIME  2020:07:20:23:24:12 longmc N 5 e 17.11 S 0.79 U 1.54 P 13% 
M 73600 F 111 R 30867 W 0 c 319 w 50082 I 48874 O 142592 L 42.23 41.81 
41.92

@#@FSLOADPOST 2020:07:20:23:24:29 longmc N 5 42.24 41.84 41.92
Linux c5-57 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s KG01_Run1.long.KG01_Run1_base exited with ERRORS at Mon 
20 Jul 23:24:29 CEST 2020


To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting




#New# invocation of recon-all





On 17/07/2020 16:28, Douglas N. Greve wrote:
I think you might have found a bug when a cross subject has more than 
one input. Can you download

https://gate.nmr.mgh.harvard.edu/safelinks/greve/longmc
Copy it to $FREESURFER/bin (make a copy of the one that is there)
Then re-run?
thanks


On 7/16/2020 11:57 AM, Knut J Bjuland wrote:


External Email - Use Caution

Thanks
Sure,

Here is the log file.

Knut Jørgen


On 16/07/2020 16:12, Douglas N. Greve wrote:

Can you send the log file?

On 7/15/2020 1:51 PM, Knut J Bjuland wrote:


External Email - Use Caution

Dear freesurfer experts

I was able to run the same subects on the longitudinal stream 
using FS 6 , but when I use FS7.1 I got this error


RROR: Number of filenames for --iscalein should agree with number 
of init LTAs (--ixforms)!

ERROR:
@#@FSTIME  2020:07:15:18:43:31 longmc N 5 e 1.75 S 0.47 U 0.15 P 
35% M 2444 F 88 R 26962 W 0 c 321 w 33906 I 19328 O 14 L 31.52 
31.63 31.62

@#@FSLOADPOST 2020:07:15:18:43:33 longmc N 5 31.55 31.64 31.63
Linux c5-31 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s 007_Run1.long.007_Run1_base exited with ERRORS at Wed 
Jul 15 18:43:33 CEST 2020


Knut Jørgen Bjuland

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Re: [Freesurfer] FsAverage4 vertex coordinates

[Douglas N. Greve]

Use mris_convert to convert the white or pial surfaces to ascii

On 7/20/2020 3:41 PM, Walsh, Shane W. wrote:

Hi FreeSurfer developers,

I'm looking for the xyz coordinate table for the vertices of the 
FsAverage4 atlas. I have fMRI data that has been sampled to the 
FsAverage4 space and it would be helpful if I could understand where a 
given vertex is located in the brain in terms of coordinates. Does 
anyone on the list know where I could find this information? I imagine 
it may be in the subjects directory that comes with the FreeSurfer 
software, but I haven't been able to locate it.


Thank you for your help,
Shane


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Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

[Douglas N. Greve]

To answer #2, You should definitely not mix them. For #1, the study has 
not been done. In principle, FLAIR is better because T2 has both bright 
and dark in the extra cerebrum whereas FLAIR has only dark. That said, 
there might be other factors that could make FLAIR worse.


On 7/20/2020 12:13 PM, Batra, Vinita R. wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my 
study,


and I want to use them to improve pial surface reconstruction during 
recon-all


as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?

2) Some subjects (< 10%) do not have a FLAIR image, and others do not 
have a


T2. Do you think that it is fine to use FLAIR for some subjects, and 
T2 for others, in the same study? We will perform manual QC after the 
recon-all run and exclude bad quality images so I wanted to hear your 
opinion.


Best,

VB


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Re: [Freesurfer] Flag(s) for parallel processing

[Douglas N. Greve]

No, I don't think that 3 hour number was ever accurate.

On 7/20/2020 10:12 AM, Billah, Tashrif wrote:

Hi Douglas,
You asked a good question which prompted me to do an experiment with 
just "-threads 8 -itkthreads 8".
The run time has been quite slower (~8 hours) compared to ~5 hours it 
took with "-parallel -openmp 8".
I agree with you about the underestimation of run time with the latter 
flags in that page. Though the page stipulates
3 hours, I have never been able to get a freesurfer done in less than 
5 hours. Maybe it is related to the resolution of my

data?
-Tashrif
.
-parallel -openmp 4
should run things with 4 processors and parallelize across hemi where 
itcanThe run time on that page is probably not accurate. But is it 
fasterwhen you use those options?

On 7/16/2020 11:47 PM, Billah, Tashrif wrote:

This
says"-openmp
 after -parallel",
thissays
"export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2", while
this says
"--threadsnthreads" for parallel processing. I want to run
recon-all and wantall processes under recon-all to be
parallelized. Which one(s) of theabove flags should I provide with
recon-all? Please note that thevalues are not my interest, the
flags are. I know the proper values Ishould choose for the flags
on my machines. So far I have been trying "-parallel -openmp 4"
option only but my runtime stays over 5 hours contrary to less
than 3 hours stipulated inthe documentation.

-Tashrif
.

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