[Freesurfer] Error during skullstripping: numerical result out of range

[Hye Min Shin]

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Hi experts,

While running recon-all on subjects with 3T T1 scans, I ran into an error
with one subject during skullstripping stage. Recon-all was running with 3T
flag.

The error message is the following:

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
GCAhistoScaleImageIntensities: could not find wm peak
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=10.0
skull bounding box = (46, 56, 29) --> (216, 255, 255)
using (103, 122, 142) as brain centroid...
mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find
MRI wm
before smoothing, mri peak at 73
robust fit to distribution - 72 +- 7.4
distribution too broad for accurate scaling - disabling
WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100,
mri_peak=108
after smoothing, mri peak at 0, scaling input intensities by inf
Numerical result out of range

I tried the following suggestion in
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html
but to no avail.

It's just strange because only one subject has this issue and the subject's
scan looks fine- no part of the brain seems cutoff.

Any suggestions would be helpful.
Best,
Julia Shin
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[Freesurfer] Problem with dcmunpack on freesurfer

[Praveen Raghunathan]

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Hi Freesurfer developers,

Sorry if I'm making a simple mistake that I've overlooked. I am currently
trying to do the freesurfer tutorials available at
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials and am having problems
with the dcmunpack command on freesurfer. Whenever I try to run the
dcmunpack script (whether it's dcmunpack -help or dcmunpack -src .
-scanonly scan.log), I get the following error message :

bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter:
No such file or directory

I have installed freesurfer, added the license and am able to use freeview
to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm
not able to find any online documentation on how to install or source that
particular script either. I've searched the list archive and no similar
errors have been reported. Please advise and let me know what I should do
or what I'm doing wrong.

I am currently running freesurfer on a virtual machine using Oracle
Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm
using is:
Ubuntu 20.04.1 LTS
and the freesurfer version is:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
I am using a Bash shell to run the commands.

Thank you so much for your help! Please let me know if you need any other
information.

Sincerely
Praveen V. Raghunathan
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[Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[李梦君]

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Dear FreeSurfer Developers:


   I compared the thickness, area, volume in the mild traumatic brain injury 
patients with health control by FreeSurFer, and found a statistic difference 
region in the cortex area, I defined the statistic difference region as a label 
on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The 
label defined on the fsaverage was mapped onto all subjects successfully, and 
the label in subjects matched well with the inflated cortex of subjects in 
Freeview  Then the area value of the label in every single subjects was 
extracted, and I found that there is no statistic difference in the area value 
between the mild traumatic brain injury patients and health control. I have 
checked the segmentation of every subjects and it was a good job done by 
FreeSurFer. 


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.


Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University___
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[Freesurfer] why can't I receive a reply from others in my mailbox?

[1248742467]

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Hello, After i asked a question, why can't I receive a reply from others 
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[Freesurfer] replace the vertex_label_index in .annot file

[1248742467]

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hello,
Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id 
and vertex_label,
'
from freesurfer_surface import Surface
from freesurfer_surface import Label
from freesurfer_surface import Annotation


surface = Surface.read_triangular('rh.white')
surface.load_annotation_file('rh.aparc.a2009s.annot')
with open("rhlabels.txt","w") as f:
for vertex_index, vertex in enumerate(surface.vertices):
vertex_label_index = surface.annotation.vertex_label_index[vertex_index]
vertex_label = surface.annotation.labels[vertex_label_index]
#print(vertex_index, vertex, vertex_label)
#f.write("vertex_index:{}  vertexlabel:{} \n".format(vertex_index, 
vertex_label))
f.write("vertex_index:{} vertex_label:{}\n".format(vertex_index, 
vertex_label))
'
the output:vertex_index:0  vertexlabel:Label(name=S_precentral-sup-part, 
index=70, color=#1514c8) 
and the label_index obtained after a certain algorithm was updated to replace 
the vertex_labe_index in rh.aparc.2009s.annot, and then load the result with 
freeview. But I don't know how to replace the vertex_label_index value in 
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Re: [Freesurfer] Tracula error: run list is longer than subject list

[Yendiki, Anastasia]

Make sure to use "subjlist", not "sublist". If that is not the issue, then 
please attach your log file and configuration file - it's hard to guess the 
issue without more information.

Best,
Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shanika Jayakody 

Sent: Monday, October 19, 2020 2:43 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Tracula error: run list is longer than subject list


External Email - Use Caution

Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi
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Re: [Freesurfer] surf pial_lgi not created in version 7.1.0

[Kathy L. Pearson]

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I am getting this error near the tail of the 7.1.0 recon-all.log file just 
before exit:
ERROR: find_corresponding_center_FSformat did not complete successfully!

At this link from May 13:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66255.html
I see that you have posted in reference to a similar question:

https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m

If this is different from the 7.1.0 distribution's file in the matlab directory
   May 11 10:04 find_corresponding_center_FSformat.m
please let me know what authentication login/password combination is needed to 
access this to see if it  will fix my errors.

Is this file updated in the newer 7.1.1?

Thanks,

Kathy

>Douglas N. Greve Mon, 19 Oct 2020 07:42:01 -0700
> Can you send the recon-all.log file?

__
From: Kathy L. Pearson 
Sent: Friday, October 9, 2020 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: surf pial_lgi not created in version 7.1.0

No, it does not exist, and my question is why not in 7.1.0 when it is created 
with the same two commands in 5.3.0?

Thanks,

Kathy


> Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700
> does that file exist?


From: Kathy L. Pearson
Sent: Thursday, October 8, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: surf pial_lgi not created in version 7.1.0

In freesurfer version 5.3.0, I can successfully run:
recon-all -autorecon-all -mprage -s $subj -qcache -localGI
recon-all -s $subj -qcache -measure pial_lgi

However, the same commands with 7.1.0 give an error after this last of a number 
of generated statements and no surf/*pial_lgi output:
mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out 
lh.pial_lgi.fsaverage.mgh
nsubjects = 1
 ERROR: cannot find subjects/147608/surf/lh.pial_lgi

Is a new command needed for version 7.1.0?

Thanks,

Kathy Pearson


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Re: [Freesurfer] Exited with errors, segmentation fault

[Hoopes, Andrew]

Hi Julia,

This is a small bug that's been fixed in the 7.1.1 patch release. I would 
recommend updating freesurfer versions (there will be no differences in 
recon-all results).

Best,
Andrew

On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Julia Lam"  wrote:

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Hi,
In one of 56 volumes, recon-all exited with errors (segmentation fault). I 
tried to rerun but received the same result. How can this be solved?

I’ve attached the recon-all.log and recon-all.error.

I am looking forward to your reply.

Kind regards,
Julia Lam





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[Freesurfer] Tracula error: run list is longer than subject list

[Shanika Jayakody]

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Hello,

I have been trying to run trac-all on a DWI of a participant, but I keep 
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one 
subject so I am not sure what the error is about.
I wonder if anyone can help me figure out a solution.

Many thanks
Oshadi
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[Freesurfer] fwhm values for gyrification index analysis

[vittal korann]

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Hi Doug

I'm analyzing the gyrification values between schizophrenia and healthy
volunteers. While performing group analysis in QDEC, I encountered an error
when setting the smoothing (fwhm) parameter to 25.
Here is the error message from the terminal output

> fwhm.dat: 66.612034, rounded to 67
> ERROR: fwhm out-of-range (< 1 or > 30)!
> Error in Monte Carlo simulation: Error running mri_surfcluster!


The same error persists for all smoothing values i.e. 5,10,15,20,25.
QDEC works when I set fwhm to zero units. Why it is like this? And what is
the ideal value of smoothing kernel (fwhm) for gyrification analysis?

With thanks
Korann
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Re: [Freesurfer] Problem of the Mapping Label to the Subject

[李梦君]

External Email - Use Caution

Thank you very much, I will try surface analysis with command in 7.1.1 version


-原始邮件-
发件人:"Wang, Ruopeng" 
发送时间:2020-10-20 00:39:56 (星期二)
收件人: "李梦君" 
抄送: "Freesurfer support list" 
主题: Re: [Freesurfer] Problem of the Mapping Label to the Subject

Sorry I was commenting on the screenshots in your previous email. I thought 
they were from freeview. We do not support Qdec anymore in 7.x versions.


Ruopeng



On Oct 19, 2020, at 11:09 AM, 李梦君  wrote:



External Email - Use Caution



Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command 
when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in 
the 7.1.1 version.


Best wishes
Mengjun Li



-原始邮件-
发件人:"Wang, Ruopeng" 
发送时间:2020-10-19 21:07:45 (星期一)
收件人: "Freesurfer support list" 
抄送:
主题: Re: [Freesurfer] Problem of the Mapping Label to the Subject

I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. 
Would it be possible for you to try FS 7.1.1? A quick workaround you may try 
first is to change the offset for the inflated surface to 0 0 0 in freeview 
6.0.0.


Best,
Ruopeng



On Oct 19, 2020, at 2:38 AM, 李梦君  wrote:



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Dear FreeSurfer Developers:


  My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central 
South University. I compared the cortex, area, volume in the mild traumatic 
brain injury patients with health control by the FreeSurFer and found the 
problem when mapping label to the single subjects.


  There is statistic difference in the area and volume between the mild 
traumatic brain injury patients and the health control, I defined the statistic 
difference region as a label on the fsaverage and mapped this label to subjects 
by the Qdec. Although the label defined on the fsaverage was mapped onto all 
subjects successfully,the label in the subjects did not match well with the 
inflated cortex of the subjects. At the same time, the volume and area value of 
the label have been extracted in every subject and I found that there is no 
statistic difference between the mild traumatic brain injury patients and 
health control. I have checked the segmentation of every subjects and it was a 
good job done by FreeSurFer. Attached figures illustrated the label mapping 
results.


Figure 1: the label defined on the fsaverage
Figure 2: the lateral view of the label in the subjects
Figure 3: the inferior view of the label in the subjects


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra


  I am sending this email for help since I am not sure how to fix this problem. 
Looking forward to hearing your reply! Thank you very much!


Best wishes
Mengjun Li
Second Xiangya Hospital 
Central South University.










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Re: [Freesurfer] Problem of the Mapping Label to the Subject

[Wang, Ruopeng]

Sorry I was commenting on the screenshots in your previous email. I thought 
they were from freeview. We do not support Qdec anymore in 7.x versions.

Ruopeng

On Oct 19, 2020, at 11:09 AM, 李梦君 
mailto:meng...@csu.edu.cn>> wrote:


External Email - Use Caution

Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command 
when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in 
the 7.1.1 version.

Best wishes
Mengjun Li



-原始邮件-
发件人:"Wang, Ruopeng" mailto:rwa...@mgh.harvard.edu>>
发送时间:2020-10-19 21:07:45 (星期一)
收件人: "Freesurfer support list" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
抄送:
主题: Re: [Freesurfer] Problem of the Mapping Label to the Subject

I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. 
Would it be possible for you to try FS 7.1.1? A quick workaround you may try 
first is to change the offset for the inflated surface to 0 0 0 in freeview 
6.0.0.

Best,
Ruopeng

On Oct 19, 2020, at 2:38 AM, 李梦君 
mailto:meng...@csu.edu.cn>> wrote:


External Email - Use Caution




Dear FreeSurfer Developers:

  My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central 
South University. I compared the cortex, area, volume in the mild traumatic 
brain injury patients with health control by the FreeSurFer and found the 
problem when mapping label to the single subjects.

  There is statistic difference in the area and volume between the mild 
traumatic brain injury patients and the health control, I defined the statistic 
difference region as a label on the fsaverage and mapped this label to subjects 
by the Qdec. Although the label defined on the fsaverage was mapped onto all 
subjects successfully,the label in the subjects did not match well with the 
inflated cortex of the subjects. At the same time, the volume and area value of 
the label have been extracted in every subject and I found that there is no 
statistic difference between the mild traumatic brain injury patients and 
health control. I have checked the segmentation of every subjects and it was a 
good job done by FreeSurFer. Attached figures illustrated the label mapping 
results.

Figure 1: the label defined on the fsaverage
Figure 2: the lateral view of the label in the subjects
Figure 3: the inferior view of the label in the subjects

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra

  I am sending this email for help since I am not sure how to fix this problem. 
Looking forward to hearing your reply! Thank you very much!

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University.





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Re: [Freesurfer] Creating ROI from sig.mgh

[Douglas N. Greve]

Try using the correction for multiple comparisons (mri_glmfit-sim). Set 
the CWP threshold to 1.0 to get all the clusters. It will create a table 
with GI values for each cluster. Run mri_glmfit-sim with --help and/or 
look on line to get more info



On 10/14/2020 3:55 PM, Basavaraju, Rakshathi wrote:


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I have run a vertex based gyrification index analysis. Now I want to 
create a mask/ROI from the cluster of vertices which are above the 
threshold of 3 in sig.mgh file (p<0.001). Which command should I use 
for this purpose? Is it mri_mask? or mri_vol2roi?


Next how do I extract the GI value (a numeric) from the above obtained 
ROI from individual scans?


If anyone has done anything similar with thickness or volume (which I 
am sure many would have done), it would be helpful if you guided me. 
Eagerly waiting for your response.


Thanks,
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute for Research on Alzheimer's Disease and the Aging Brain
Columbia University Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu 
_https://indiaalliance.org/fellow/rakshathi-basavaraju_


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Re: [Freesurfer] Problem of the Mapping Label to the Subject

[Douglas N. Greve]

There is no QDEC in 7.X, we have abandoned it.

On 10/19/2020 11:09 AM, 李梦君 wrote:


External Email - Use Caution

Thanks for your help, I have tried FS 7.1.1, while there is no Qdec 
command when I tried FS 7.1.1 in the terminal window. How should I 
start the Qdec in the 7.1.1 version.


Best wishes
Mengjun Li



-原始邮件-
*发件人:*"Wang, Ruopeng" 
*发送时间:*2020-10-19 21:07:45 (星期一)
*收件人:* "Freesurfer support list" 
*抄送:*
*主题:* Re: [Freesurfer] Problem of the Mapping Label to the Subject

I think this is a bug in freeview from FS 6.0.0 that has been
fixed in 7.x. Would it be possible for you to try FS 7.1.1? A
quick workaround you may try first is to change the offset for the
inflated surface to 0 0 0 in freeview 6.0.0.

Best,
Ruopeng


On Oct 19, 2020, at 2:38 AM, 李梦君 mailto:meng...@csu.edu.cn>> wrote:

External Email - Use Caution





Dear FreeSurfer Developers:

My name is Mengjun Li, I am a MD in the Second Xiangya
Hospital, Central South University. I compared the cortex,
area, volume in the mild traumatic brain injury patients with
health control by the FreeSurFer and found the problem when
mapping label to the single subjects.

There is statistic difference in the area and volume
between the mild traumatic brain injury patients and the
health control, I defined the statistic difference region as
a label on the fsaverage and mapped this label to subjects by
the Qdec. Although the label defined on the fsaverage was
mapped onto all subjects successfully,the label in the
subjects did not match well with the inflated cortex of the
subjects. At the same time, the volume and area value of the
label have been extracted in every subject and I found that
there is no statistic difference between the mild traumatic
brain injury patients and health control. I have checked the
segmentation of every subjects and it was a good job done by
FreeSurFer. Attached figures illustrated the label mapping
results.

Figure 1: the label defined on the fsaverage
Figure 2: the lateral view of the label in the subjects
Figure 3: the inferior view of the label in the subjects

FreeSurfer
version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra

I am sending this email for help since I am not sure how to
fix this problem. Looking forward to hearing your reply!
Thank you very much!

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University.





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Re: [Freesurfer] Error sending tcl command

[Douglas N. Greve]

We are no longer support tksurfer. You can try using freeview. If you 
run tksurferfv, it will run freeview with most of the tksurfer command 
line options


On 10/14/2020 11:42 PM, Kothapalli, Satya wrote:


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Hi Expert,

I am trying to render the surface maps using tksurfer command in the 
freesurfer VDI. The  data was rendered on the brainmask , however the 
options for this maps are not appeared (as shown in the figure).


Further I found the error message on the command window that related 
to tcl command as shown here. I would appreciate if you can provide 
the possible solution to this issue.


Thanks,

Satya.



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the contents of this information is strictly prohibited. If you have 
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Re: [Freesurfer] Help with creating contrast matrix - 6 classes and 3 variables

[Douglas N. Greve]

With 6 classes and 3 variables, you will have 24 regression coefficients 
and so 24 items in your contrast matrix (so good, so far). The order will be

1. MaleMaxT-Offset
2. MaleKahn-Offset
3.
4.
5.
6.
7. MaleMaxT-AgeSlope
8
9
10
11
12
13 MaleMaxT-HRSD_Reduction-Slope
14 MaleKahn-HRSD_Reduction-Slope
15
16
17
18 FemaleNone-HRSD_Reduction-Slope
19 MaleMaxT-SessionNumber-Slope
20
...

So all the HRSD_Reduction-Slopevariables are in items 13-18, so you set 
them all to 1 and let the others be 0, which is what you have.


Bottom line: you have done it correctly.

On 10/13/2020 7:52 PM, Paul Dhami wrote:


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Dear Freesurfer community,

I am having trouble with my contrast matrix, and would greatly 
appreciate any help with this.


I have 2 categorical variables, sex (2 levels) and training type (3 
levels).


I also have three (continuous) variables: Age, percentage reduction in 
depression scores, and number of sessions.


I would like to assess the correlation between cortical thickness and 
% reduction in depression scores, while accounting for the effects of 
sex, training type, age, and number of sessions as nuisance variables.


Below is 1) my command line, 2) the FSGD fiile, and 3) the design matrix

1.

mri_glmfit.bin --y MDD-lh-thickness.mgh --fsgd 
Reduction_Correlation.fsgd.txt --C 
ME_ReductionCorrelation_Contrast.txt --fwhm 20 --surf fsaverage lh 
--glmdir /Users/prabhjotdhami/Desktop/CorticalThickness/Data/myGLM



2.


GroupDescriptorFile 1
Title MDD_correlation
Class MaleMaxT
Class MaleKahn
Class MaleNone
Class FemaleMaxT
Class FemaleKahn
Class FemaleNone
Variables Age HRSD_Reduction SessionNumber
Input yct-001 FemaleMaxT 24 62.5 20
Input yct-002 MaleKahn 18 70 20
Input yct-004 MaleMaxT 21 50 20
Input yct-005 MaleMaxT 24 25 20
Input yct-006 FemaleKahn 24 65.2173913 20
Input yct-012 FemaleKahn 17 71.42857143 20
Input yct-013 MaleMaxT 22 53.84615385 20
Input yct-014 FemaleMaxT 19 63.63636364 20
Input yct-015 FemaleMaxT 16 80.95238095 20
Input yct-016 FemaleKahn 24 65.2173913 20
Input yct-017 FemaleKahn 22 55 20
Input yct-018 FemaleMaxT 18 82.60869565 20
Input yct-019 MaleKahn 16 85 20
Input yct-020 FemaleMaxT 22 85 20
Input yct-021 MaleMaxT 24 81.81818182 20
Input yct-022 FemaleKahn 21 70.8333 20
Input yct-023 FemaleMaxT 20 52 20
Input yct-024 MaleKahn 16 73.68421053 20
Input yct-025 MaleKahn 21 23.80952381 20
Input yct-026 FemaleMaxT 20 78.26086957 20
Input yct-027 FemaleMaxT 17 20 20
Input yct-030 FemaleMaxT 19 52 20
Input yd-p002 MaleNone 20 54.54545455 10
Input yd-p006 FemaleNone 23 30 10
Input yd-p008 MaleNone 22 44 10
Input yd-p010 FemaleNone 16 50 10
Input yd-p014 FemaleNone 22 3.846153846 10
Input yd-p015 MaleNone 19 10 10
Input yd-p022 FemaleNone 24 37.03703704 10
Input yd-p026 FemaleNone 21 47.61904762 10
Input yd-p027 MaleNone 23 31.57894737 10
Input yd-p032 FemaleNone 21 75 10
Input yd-p033 MaleNone 24 22. 10
Input yd-p034 FemaleNone 22 25 10
Input yd-p035 MaleNone 24 30.43478261 10
Input yd-p047 MaleNone 16 78.26086957 10
Input yd-p048 MaleNone 17 20 10
Input yd-p051 FemaleNone 18 45 10
Input yd-p052 FemaleNone 20 47.82608696 10


3.

0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0 0


Any help would be greatly appreciated.


Thank you,

Paul



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Re: [Freesurfer] Estimating the memory footprint of Longitudinal Stream?

[Douglas N. Greve]

I don't know. Each command will have an fs_time output which will have a 
measure of the peak memory used, though it is not super accurate. 
Alternatively, I could add something to mri_fuse_segmentations to 
periodically print out the peak memory usage


On 10/13/2020 3:01 PM, Paul Wighton wrote:


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Hi FreeSurfers,

Is there any guidance on how to estimate the memory footprint of the 
Longitudinal steam?


We are trying to process the MacLaren test-retest dataset [1] (40 
timepoints per subject) with the longitudinal stream in v7.1.1 and are 
running into memory errors during `mri_fuse_segmentations`.


Thanks,

-Paul

[1]: https://openneuro.org/datasets/ds000239/versions/1

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Re: [Freesurfer] Problem of the Mapping Label to the Subject

[李梦君]

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Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command 
when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in 
the 7.1.1 version.


Best wishes
Mengjun Li



-原始邮件-
发件人:"Wang, Ruopeng" 
发送时间:2020-10-19 21:07:45 (星期一)
收件人: "Freesurfer support list" 
抄送:
主题: Re: [Freesurfer] Problem of the Mapping Label to the Subject

I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. 
Would it be possible for you to try FS 7.1.1? A quick workaround you may try 
first is to change the offset for the inflated surface to 0 0 0 in freeview 
6.0.0.


Best,
Ruopeng



On Oct 19, 2020, at 2:38 AM, 李梦君  wrote:



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Dear FreeSurfer Developers:


  My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central 
South University. I compared the cortex, area, volume in the mild traumatic 
brain injury patients with health control by the FreeSurFer and found the 
problem when mapping label to the single subjects.


  There is statistic difference in the area and volume between the mild 
traumatic brain injury patients and the health control, I defined the statistic 
difference region as a label on the fsaverage and mapped this label to subjects 
by the Qdec. Although the label defined on the fsaverage was mapped onto all 
subjects successfully,the label in the subjects did not match well with the 
inflated cortex of the subjects. At the same time, the volume and area value of 
the label have been extracted in every subject and I found that there is no 
statistic difference between the mild traumatic brain injury patients and 
health control. I have checked the segmentation of every subjects and it was a 
good job done by FreeSurFer. Attached figures illustrated the label mapping 
results.


Figure 1: the label defined on the fsaverage
Figure 2: the lateral view of the label in the subjects
Figure 3: the inferior view of the label in the subjects


FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra


  I am sending this email for help since I am not sure how to fix this problem. 
Looking forward to hearing your reply! Thank you very much!


Best wishes
Mengjun Li
Second Xiangya Hospital 
Central South University.










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Re: [Freesurfer] amygdala segmentation on anatomy

[Douglas N. Greve]

You have to run recon-all on your T1-weighted image (see the tutorials 
on the wiki), then run the hippo/amyg segmentation as found here

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


On 10/13/2020 12:32 PM, Elena Aggius-Vella wrote:


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Dear freesurfer,

This is Elena Aggius Vella.
I'm writing to ask for your help.
I need to do amygdala segmentation based on anatomy I see 
freesurfer has a nice tool to do it, but i'm new in freesurfer. Is it 
possible to have any help on this?


many many thanks
elena

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Re: [Freesurfer] Qdec - talairach to vertex for display purposes

[Douglas N. Greve]

We don't use qdec anymore, so I can't remember what the interface is 
like. You can transfer your coordinates to fsaverage space, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

and then go to that point in freeview


On 10/13/2020 9:45 AM, Paul Dhami wrote:


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Dear Freesurfer community,

I have an experiment in which participants received brain stimulation 
using anatomical coordinates which I have in talairach space.


I have run a whole-brain analysis using qdec, and I have a surviving 
cluster. For display purposes, I would like to show that the 
coordinates that were stimulated fall within this cluster.


Is there a way to plug in talairach coordinates within the qdec 
display so that the cross hair (or some sort of other marking) appears 
at that specific corresponding vertex?


Thank you,
Paul

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Re: [Freesurfer] The usage about annotation view

[Douglas N. Greve]

I don't understand what you are saying. Can you elaborate?

On 10/13/2020 8:31 AM, 1248742467 wrote:


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hello, FreeSurfer

I have loaded rh.pial and rh.aparc.2009s.annot, why my version does 
not have the label view option that can see the annotation? Is it a 
version issue? My FreeSurfer 
version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c


Looking forward to your reply




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Re: [Freesurfer] Put the updated vertex_label into .annotation

[Douglas N. Greve]

Use mris_label2annot
Run with --help to get examples

On 10/13/2020 8:22 AM, 1248742467 wrote:


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hello, After I updated the vertex_label of rh.aparc.a2009s.annot with 
an algorithm, now I want to replace the vertex_label in the .annot 
with the updated vertex_label, mainly to see the effect of the 
segmentation, do you know what to do ?

if you know, please give me a example

looking forward to your reply

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Re: [Freesurfer] asegstats2table error with options --etiv and --no-vol-extras

[Douglas N. Greve]

What happens if you don't include --segno ?

On 10/13/2020 8:11 AM, Rovai Antonin wrote:
>  External Email - Use Caution
>
> Hello,
>
> when using asegstats2table with the two flags --etiv and --no-vol-
> extras, I get the following error:
>
> ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list
>
> It seems computing the ratio of volumes to etiv needs etiv to be
> included in the list (which by the way is not very useful because it is
> 100% by definition), but is there a way to get the ratios without
> including all the "extra" volumes?
>
> For instance using
>
> asegstats2table --tablefile "output.txt" --no-vol-extras --etiv --segno
> 225
>
> I would expect to get the volume of CC_Anterior in % of etiv.
>
> Thanks for your help
>
> Antonin
>
> Hôpital Erasme - ULB
> Cliniques universitaires de Bruxelles
> Route de Lennik 808 - B - 1070 Bruxelles
> S www.erasme.ulb.ac.be
>
> Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
>
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Re: [Freesurfer] Moving .nii atlas to surface space and create .annot file

[Douglas N. Greve]

On 10/13/2020 5:42 AM, Maron M. wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Team,
>
> I need to move an atlas file, Shen268 in 2mm 
> (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz)
>  from volumetric into surface space in order to do some analysis in MATLAB 
> with it. Specifically, I need the atlas file as .annot and a .sphere (I think 
> this would be from the anatomical template).
>
> So far, I have not succeeded.
> I believe it is some combination of recon-all, mri_vol2surf and 
> mris_seg2annot, however the details are unclear.
>
> I think the initial problem is with the recon all. In this question 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63687.html) 
> it says I should recon-all the "anatomical template". Could you elaborate 
> which template that is? Its not the atlas file itself, but just some T1 in 
> the same space?
>
> And that will give me the file necessary for the --reg command in 
> mri_vol2surf, I guess?
>
> Sofar, I think this is what I have to do:
>
> 1)
> Recon-all -all -i "anatomical_template" (I am stuck here already, since I 
> don't know what to recon-all here...)
Yes, the template is an anatomical T1-weighted image in the same space 
as your atlas. Usually, this would be a volume that you would register 
your individual subjects to to get them into the atlas space (eg, the 
MNI152 volume). Run recon-all on that.

> 2)
> mri_vol2surf --src atlas_file.nii --out outputfile_rh.mgz --hemi rh 
> --projfrac 0.5 (--trgsubject fsaverage or —reg register.dat from recon-all?)
Use --regheader subject
where subject is the name of the subject you gave during recon-all. If 
you need to have the output in fsaverage space, you can add --trgsubject 
fsaverage
>
> 3)
> mris_seg2annot --seg outputfile_rh.mgz --s fsaverage --h rh --ctab-auto --o 
> atlas_rh.annot
This should work (but use subject instead of fsaverage if subject used 
in mri_vol2surf). Also, you'll probably want to call the output 
rh.atlas.annot
>
>
> I would be very thankful for any suggestions and support.
> Best and thanks a lot!
>
>
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Re: [Freesurfer] display results with tksurfer

[Douglas N. Greve]

Not sure, we don't use tksurfer that much anymore. Have you tried 
freeview? You can run freeview with tksurferfv and the same tksurfer 
arguments (makes it easier)


On 10/13/2020 5:03 AM, Marina Fernández wrote:


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Dear Freesurfer experts,

I would like to modify the values of the colorbar scale to display 
results in the inflated surface with tksurfer, in such a way that 
displayed values in the colorbar range from the minimum t- value 
detected to the maximum t value detected. I have tried to use the 
-fminmax flag, but the colorbar scale shows values from 0 to the 
maximum t value. Is it possible to limit values of the colorbar scale 
to min-max significant t values?


On the other hand, is it possible to invert the colors of the colorbar 
scale (e.g., red for higher t values and yellow for lower t values)?


Thank you in advance.

Best regards,
Marina

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Re: [Freesurfer] mapping function of 3d coordinates of brain surface to latitude and longitude of a sphere

[Douglas N. Greve]

No sure what you are trying to do. Each  vertex on the surface has 
several  coordinates associated with it. Eg, a given vertex on the white 
surface will have a coordinate in the volume space (see 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems); that same 
vertex in the ?h.sphere.reg will have a coordinate on the sphere.


On 10/12/2020 2:13 AM, 정태곤 wrote:


External Email - Use Caution

Dear Mr.


I want to map final processed cortical thickness data of 3d coordinate 
(each point on a brain surface) again onto inflated sphere(?h.sphere)


so that cortical thickness can be represented with latitude and 
longitude of the sphere.


But I couldn't find mapping information to do so.

Could you help me with where to find map function of 3d cortical 
surface point to sphere?


I would appreciate for your help.


Thanks


PS. I couldn't find elsewhere to ask but here.

Sorry for posting on bug report.


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Re: [Freesurfer] Display results

[Douglas N. Greve]

Load it as a volume using freeview

On 10/11/2020 4:42 PM, Valentina Mancini wrote:


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Thank you for this answer.

How should I load aparc a2009+aseg.mgz for visualization and load a 
color map with p-values?



If I  load the fsaverage with the command "tksurfer", then I can only 
load the lh.aparc.a2009s.annot label but I need Desikan and Killiany 
atlas and not Destrieux atlas and also the subcortical structures. I 
couldn't find any label comprising subcortical structures.



*Da:* freesurfer-boun...@nmr.mgh.harvard.edu 
 per conto di Douglas N. Greve 


*Inviato:* venerdì 9 ottobre 2020 14:51:23
*A:* freesurfer@nmr.mgh.harvard.edu
*Oggetto:* Re: [Freesurfer] Display results
Try aparc.a2009s+aseg.mgz


On 10/9/2020 3:07 AM, Valentina Mancini wrote:


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Dear freesurfer experts,



I'm trying to display the results of a study on a brain with Desikan 
and Killiany parcellation.


Currently, I use tksurfer fsaverage, load the aparc.annot annotation, 
modify the colortable with values of interest and load it.


However, in this way I can display only cortical regions.


Any suggestions on how I could display cortical and subcortical 
regions at the same time? And where do I find an ordered list of 
cortical + subcortical structures to modify the values in each ROI?



Thank you in advance for your help.


Best,


Valentina


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Re: [Freesurfer] Error with pial delineation

[Douglas N. Greve]

That is fine. The surface has to cross the ventricle at some point

On 10/9/2020 2:09 PM, Julie Ottoy wrote:


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Dear Freesurfer team,

I have a question regarding the freesurfer delineation of the subject 
in attachment. Here the pial delineation crosses the ventricle, 
instead of being delineating around the hippocampus.
The light purple corresponds to the inferior lateral ventricle, and 
the dark purple corresponds to lateral ventricle segmentation. The 
hippocampus is the yellow segmentation.


Would it be important to fix this for regional analyses? It seems as 
though the regions themselves were correctly assigned.


What would be the appropriate way to fix this? Could control points be 
of any help?


Thank you!
Best regards
Julie

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Re: [Freesurfer] surf pial_lgi not created in version 7.1.0

[Douglas N. Greve]

Can you send the recon-all.log file?

On 10/9/2020 12:47 PM, Kathy L. Pearson wrote:
>  External Email - Use Caution
>
> No, it does not exist, and my question is why not in 7.1.0 when it is created 
> with the same two commands in 5.3.0?
>
> Thanks,
>
> Kathy
>
>
>> Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700
>>  does that file exist?
> 
> From: Kathy L. Pearson
> Sent: Thursday, October 8, 2020 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: surf pial_lgi not created in version 7.1.0
>
> In freesurfer version 5.3.0, I can successfully run:
>  recon-all -autorecon-all -mprage -s $subj -qcache -localGI
>  recon-all -s $subj -qcache -measure pial_lgi
>
> However, the same commands with 7.1.0 give an error after this last of a 
> number of generated statements and no surf/*pial_lgi output:
>  mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage 
> --out lh.pial_lgi.fsaverage.mgh
>  nsubjects = 1
>   ERROR: cannot find subjects/147608/surf/lh.pial_lgi
>
> Is a new command needed for version 7.1.0?
>
> Thanks,
>
> Kathy Pearson
>
>
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Re: [Freesurfer] recon-all -s -autorecon2-cp -autorecon3 error

[Douglas N. Greve]

Those control points are still in gray matter.
Please remember to post to the list, thanks

On 10/9/2020 11:18 AM, Kazuki Sakakura wrote:


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Thank you for continuously helping me.

With your comment, I performed to put some control points in WM 
(attached image).

However, the error was the same as before.

Like I said before, I performed infant recon-all and there were some 
slight defects in the medial temporal area (arrow).  Therefore I tried 
to modify the surface with control points.  Is this a reason why 
"autorecon2-cp -autorecon3" command had an error? If so, Do you know 
any ways to modify the surface for infant recon-all subjects?


Thank you.
Best Regards

Kazuki Sakakura



*From:* Douglas N. Greve 
*Sent:* Friday, October 9, 2020 8:47 AM
*To:* Kazuki Sakakura 
*Subject:* Re: [Freesurfer] recon-all -s  -autorecon2-cp 
-autorecon3 error
Those are all in gray matter. You need to make sure that they are all 
in voxels that are clearly white matter


On 10/8/2020 11:25 AM, Kazuki Sakakura wrote:


External Email - Use Caution

Thank you for replying.
I'm sure I put control points in WM as the attached picture.

I performed infant recon-all and there were some slight defects in 
the medial temporal area (arrow).  Therefore I tried to modify the 
surface with control points.  Is this a reason why "autorecon2-cp 
-autorecon3" command had an error? If so, Do you know any ways to 
modify the surface for infant recon-all subjects?


Thank you.
Best Regards

Kazuki Sakakura

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 on behalf of Douglas 
N. Greve  

*Sent:* Wednesday, October 7, 2020 10:17 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 
*Subject:* Re: [Freesurfer] recon-all -s  -autorecon2-cp 
-autorecon3 error



[EXTERNAL]

I've never seen that one before. Can you post pictures of where you 
put the control points? Are you sure you put them in voxels that are 
clearly WM?


On 10/6/2020 4:33 PM, Kazuki Sakakura wrote:


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Hello FreeSurfer Developers,

I'm attempting to compute recon-all after putting control point, but 
for some of my subjects I get the attached error when I run the 
recon-all -s  -autorecon2-cp -autorecon3 command.




I've searched the list and no similar errors have been reported. 
Does 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-v5.3.0


2) Platform: Ubuuntu 14.04

3) recon-all.log: see attached


Best Regards,

Kazuki Sakakura



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Re: [Freesurfer] Seed region in anatomical data for resting state fMRI data

[Douglas N. Greve]

On 10/8/2020 8:31 PM, Gwang-Won Kim wrote:


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Hi there,

I obtained a seed region (left superior frontal)from anatomical 
data to process resting state fMRI data as follows: fcseed-sess -o 
lh.SFC.dat -segid 1028 -s session -fsd rest.
I wonder if what the seed region is the left superior frontal was 
correct.
Question1: Can I display the lh.SFC.dat as MR image (anatomical 
image)using Freeview?
When you run fcseeed-sess, add -make-mask to create a binary mask in the 
run folder. You can then load this onto the anatomical to verify


I'd like to obtain ROI region as a seed region from anatomical data to 
process resting state fMRI data.
Question2: How do I make the seed region if I use 8-mm radius spheres 
centered on a MNI coordinate [x=20, y=20, z=20] as the seed region.
You need to transfer those coordinates to the individual subject's 
anatomical space (see #8b from 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems), create 
your sphere in that space (mri_volsynth with spherical PDF), save this 
volume in subject/mri, then reference this volume when runing fcseed-config


Thanks,
Gwang-Won




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Re: [Freesurfer] Problem of the Mapping Label to the Subject

[Wang, Ruopeng]

I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. 
Would it be possible for you to try FS 7.1.1? A quick workaround you may try 
first is to change the offset for the inflated surface to 0 0 0 in freeview 
6.0.0.

Best,
Ruopeng

On Oct 19, 2020, at 2:38 AM, 李梦君 
mailto:meng...@csu.edu.cn>> wrote:


External Email - Use Caution




Dear FreeSurfer Developers:

  My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central 
South University. I compared the cortex, area, volume in the mild traumatic 
brain injury patients with health control by the FreeSurFer and found the 
problem when mapping label to the single subjects.

  There is statistic difference in the area and volume between the mild 
traumatic brain injury patients and the health control, I defined the statistic 
difference region as a label on the fsaverage and mapped this label to subjects 
by the Qdec. Although the label defined on the fsaverage was mapped onto all 
subjects successfully,the label in the subjects did not match well with the 
inflated cortex of the subjects. At the same time, the volume and area value of 
the label have been extracted in every subject and I found that there is no 
statistic difference between the mild traumatic brain injury patients and 
health control. I have checked the segmentation of every subjects and it was a 
good job done by FreeSurFer. Attached figures illustrated the label mapping 
results.

Figure 1: the label defined on the fsaverage
Figure 2: the lateral view of the label in the subjects
Figure 3: the inferior view of the label in the subjects

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra

  I am sending this email for help since I am not sure how to fix this problem. 
Looking forward to hearing your reply! Thank you very much!

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University.





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