Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

[Miriam Taza]

Nothing strange about them.
They’re T1w scans 1x1x1mm3

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

Sent: Thursday, July 28, 2022 1:25 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] sclimbic sometimes does not detect left basal 
forebrain

Have you looked at the input volume to see if there is anything strange about 
them? What kind of scans are you passing to it? What is the resolution?

On 7/25/2022 9:03 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were not picked 
up after running ScLimbic. These are healthy adults and their scans look good. 
Also, I noticed often when this occurs NAcc is also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending up 
smaller than they should relative to right.

Thanks,
Miriam



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[Freesurfer] Subregion Segmentation of thalamus for TRACULA

[Makenna B McGill]

Hi FreeSurfer Developers,

I'm trying to run TRACULA in FreeSurfer v7.3 on OS Monterey.

I was unable to download R2014b Runtime on my newer OS, so instead of the
segmentThalamicNuclei.sh script, I tried running the newer segmentation
tool segment_subregions thalamus (
https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation).

This was successful, but trac-all looks for the
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz file, whereas the subregion
segmentation produces the file ThalamicNuclei.FSvoxelSpace.mgz.

I'm wondering two things: (1) is the new segmentation tool compatible with
trac-all (the wiki says the results will be very close but not identical),
and (2) if so, would it be appropriate to rename/link the file so that
trac-all can find it, as this user did with the ThalamicNuclei.v13 file (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73065.html)?

Thank you in advance for any suggestions you might have, and please let me
know if anything needs clarified.

Best,
Makenna

*Makenna McGill *(she/her)
Doctoral Student in Clinical Psychology
University of Texas at Austin
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Re: [Freesurfer] Problem with hypothalamus subunits?

[Zeng, Victor (BIDMC - Keshavan - Psychiatry)]

External Email - Use Caution

If the brain scans went through successfully already, in an older dev version, 
do they need to be reprocessed?

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday, July 28, 2022 11:28 AM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] Problem with hypothalamus subunits?

Thanks for reporting this bug, Victor. I just fixed it. The fix will be 
propagated to the development version in the next couple of days but, if you 
want, you can keep using the version you’ve got by adding the flag --crop 1000  
(where 1000 is a number bigger than your image size in any dimension). That 
will have the same effect as the fix.

Cheers,

Eugenio

Juan Eugenio Iglesias
http://secure-web.cisco.com/1LMNPJidJYLz4yMjaDO-plzlRUw5d2xLuSCKJ3NmoysnXsKX_MfAEVcrUs0CB40fNbG6fuxKgPPM9HejKgvkaLzMo44TzgynC3MmXr7bayyVpkSMSSzOkI-JLa6-7u9G-gfbWEYMc9BdcoomCdKvHmqEkFv0JJ7cDuYKhrMMY6lCTtqi789h0P5SQU4slHK0PJg_dW9iovOeSJdUkt1FgEBBoLvtebnGanYv7zCDxkoLgfBQSPUG1id6lf4jGV1JAM3o1xWfmx_lqcULefCqLyGx-e0DgHt63f2KjZlNDyTDKd9a4pRazXN0or3xcXgXLvkdLUHDJ7t3oboc1kxdDyA/http%3A%2F%2Fwww.jeiglesias.com

On Jul 27, 2022, at 15:03, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
mailto:vz...@bidmc.harvard.edu>> wrote:

External Email - Use Caution

Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with 
running subunits:

mri_segment_hypothalamic_subunits --s 10893/
using 1 thread
/mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: 
DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has 
a more predictable return type. To obtain get_data() behavior going forward, 
use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise  as of 
version: 5.0
  volume = np.squeeze(x.get_data())
predicting 1/1

the following problem occured when preprocessing image //0893/mri/nu.mgz :
'NoneType' object is not subscriptable
resuming program execution


segmentation  saved in://10893/mri/hypothalamic_subunits_seg.v1.mgz
volumes saved in:  //10893/mri/hypothalamic_subunits_volumes.v1.csv
resampled images saved in: 
//10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz

If you use this tool in a publication, please cite:
Automated segmentation of the hypothalamus and associated subunits in brain MRI
B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias
NeuroImage 2020



Is this a problem with tensorflow? It does not seem clear. No files are 
actually being written

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
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Re: [Freesurfer] FSFAST first level covariates

[Angela Fang]

Thanks Doug. This wiki page is extremely helpful. However, my question is about 
individual subject responses. I could see how you could include a summary 
(e.g., average) value of the parametric variable across subjects in your 
“weight” column but it’s not clear to me how you could integrate individual 
subject responses to each word in the parametric modulation paradigm file? I’m 
imagining something like the FSGD file where a value is given for each subject, 
but for first-level analysis.

We have a similar design as someone else who posted a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19957.html). We 
have an event-related experiment presenting trait adjectives in terms of 
whether they describe themselves (SELF condition) or someone else (OTHER 
condition). We are interested in testing a 2x2 ANOVA to examine an interaction 
between self-relevance x emotional valence. Assuming you can’t integrate 
individual subject responses to each word in the paradigm file, would we set it 
up as follows?

“Usual” paradigm file:
0  1  2.5  1.0  SELF
2.5  0  2.5  1.0  FIXATION
5.0  1  2.5  1.0  SELF
7.5  2  2.5  1.0  OTHER

Parametric modulation paradigm file:
0  1  2.5  1.0  SELFoffset
0  2  2.5  0.8  SELFslope
0  3  2.5  1.0  VALENCEoffset
0  4  2.5  2.0  VALENCEslope

(where 0.8 reflects the percentage of time the word was endorsed as 
self-relevant and 2.0 is the average valence rating given for that word)

And then create a contrast of 2 vs 4 to test the interaction? Would testing 
contrast 1 vs 0 be a test of the main effect of self-relevance and contrast 3 
vs 0 the main effect of valence?

Thanks so much for your help!
Angela

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Thursday, July 28, 2022 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST first level covariates

Yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation

On 7/25/2022 6:56 PM, Angela Fang wrote:

External Email - Use Caution
Hi Freesurfer community,
I have run participants through an event-related fMRI task in which subjects 
rate whether trait adjectives are descriptive of themselves or not, and 
afterwards asked them to rate each trait word on emotional valence. Is it 
possible to include these individual level subjective ratings of emotional 
valence as covariates in the first level contrast in FSFAST? If so, how?
Thanks,
Angela

---
Angela Fang, Ph.D.
Assistant Professor
Department of Psychology
University of Washington
Lab website: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
www.uwconnectlab.com
Pronouns: she, her, hers




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Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

[Miriam Taza]

External Email - Use Caution

new recon all: freesurfer-darwin-macOS-dev-20220328-fc008d0
old recon all: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

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

Sent: Thursday, July 28, 2022 2:05 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

The "cvs_version" is just for that particular binary. look in 
$FREESURFER_HOME/build-stamp.txt. There should also be a build stamp file in 
$SUBJECTS_DIR/subject/scripts (should be in the recon-all.log too)

On 7/28/2022 1:41 PM, Miriam Taza wrote:

External Email - Use Caution

is it not these two lines?
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cvs_version dev
if not, for the new recon-all I also have this: 
freesurfer-darwin-macOS-dev-20220328-fc008d0

How do i check the old recon all? It was done in the past.is there a log?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, July 28, 2022 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

What version of FS are you using for recon-all?

On 7/25/2022 9:45 PM, Miriam Taza wrote:

External Email - Use Caution

I reran sclimbic and I get the same result as the first time I ran sclimbic.
I also reran recon all on one subject. The etiv now differs from the original 
recon all and the sclimbic output (although it is closer to sclimbic).

Here is the log for both recon all.

original recon all, etiv = 1169944.199744

# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt 
--subject sub-1221084
# SegVolFileTimeStamp  2018/02/28 00:18:52

new etiv = 702243.513916
# cvs_version dev
# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats 
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/Applications/freesurfer/ASegStatsLUT.txt --subject sub-1221084
# SegVolFileTimeStamp  2022/07/25 21:04:31

sclimbic etiv= 686180.089200

>From a quick glance, the other values dont seem to differ by much between 
>recons so I'm not sure why this is happening with etiv nor what value to 
>accept.

Please let me know if there is something else I can do or if you need more info.

Miriam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Miriam Taza 

Sent: Monday, July 25, 2022 2:45 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev


External Email - Use Caution

I am getting eerror: mri_segstats: could not open atlas transform file 
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
The results do agree when Re running sclimbic.

it seems that when etiv differs a bit from the median, sclimbic module 
calculates etiv to an extreme.
Is this expected to happen? I am concerned if my volumes are incorrect.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Sunday, July 24, 2022 10:38 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

I cannot replicate this on my data. The differences are rather extreme (factors 
of 3). Can you get us access to the one with the largest difference? YOu can 
also try regenerating the aseg.stats file, eg,
cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/redo.aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

[Douglas N. Greve]

those look like hcp commands so you should contact them

On 7/28/2022 2:00 PM, Ariana Fei wrote:


External Email - Use Caution

I'm attaching a list of command I used to convert freesurfer cortical 
thickness output to native space:


$Caret5_Command -file-convert -fsc2c 
"$FreeSurferFolder"/surf/"$hemisphere"h.thickness 
"$FreeSurferFolder"/surf/"$hemisphere"h.white 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -spec-file-add 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".native.c5.spec 
surface_shape_file 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -metric-set-column-name 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 
1 "$Subject"_"$Hemisphere"_Thickness
$Caret5_Command -file-convert -format-convert XML_BASE64 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -set-structure 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 
$Structure
$Caret7_Command -add-to-spec-file 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec 
$Structure 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -metric-palette 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 
MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp 
-disp-pos true -disp-neg true -disp-zero true
#cp 
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 
#commented out GW
$Caret7_Command -add-to-spec-file 
"$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure 
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii


This already gives negative cortical thickness values in native space.

Ariana



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Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

[Douglas N. Greve]

The "cvs_version" is just for that particular binary. look in 
$FREESURFER_HOME/build-stamp.txt. There should also be a build stamp 
file in $SUBJECTS_DIR/subject/scripts (should be in the recon-all.log too)


On 7/28/2022 1:41 PM, Miriam Taza wrote:


External Email - Use Caution


is it not these two lines?

# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11
greve Exp $

# cvs_version dev

if not, for the new recon-all I also have 
this: freesurfer-darwin-macOS-dev-20220328-fc008d0


How do i check the old recon all? It was done in the past.is there a log?






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


*Sent:* Thursday, July 28, 2022 1:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs 
freesurfer dev

What version of FS are you using for recon-all?

On 7/25/2022 9:45 PM, Miriam Taza wrote:


External Email - Use Caution

I reran sclimbic and I get the same result as the first time I ran 
sclimbic.
I also reran recon all on one subject. The etiv now differs from the 
original recon all and the sclimbic output (although it is closer to 
sclimbic).


Here is the log for both recon all.

original recon all, etiv = *1169944.199744*


# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11
greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent
--subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
--totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt
--subject sub-1221084
# SegVolFileTimeStamp  2018/02/28 00:18:52

new etiv = *702243.513916*
# cvs_version dev
# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum
stats/aseg.stats --pv mri/norm.mgz --empty --brainmask
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab
/Applications/freesurfer/ASegStatsLUT.txt --subject sub-1221084
# SegVolFileTimeStamp  2022/07/25 21:04:31

sclimbic etiv= *686180.089200
*

*
*
>From a quick glance, the other values dont seem to differ by much 
between recons so I'm not sure why this is happening with etiv nor 
what value to accept.

*
*
Please let me know if there is something else I can do or if you need 
more info.


Miriam

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 on behalf of Miriam 
Taza  

*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list  

*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs 
freesurfer dev


External Email - Use Caution

I am getting eerror: mri_segstats: could not open atlas transform 
file 
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm

The results do agree when Re running sclimbic.

it seems that when etiv differs a bit from the median, sclimbic 
module calculates etiv to an extreme.

Is this expected to happen? I am concerned if my volumes are incorrect.



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

*Sent:* Sunday, July 24, 2022 10:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs 
freesurfer dev
I cannot replicate this on my data. The differences are rather 
extreme (factors of 3). Can you get us access to the one with the 
largest difference? YOu can also try regenerating the aseg.stats 
file, eg,

cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum 
stats/redo.aseg.stats --pv mri/norm.mgz --empty --brainmask 
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm 
--supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
--totalgray --euler --ctab 
/usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject subject


Check the eTIV in redo.aseg.stats against that in aseg.stats, then 
re-run mri_sclimbic_seg to see if the results agree.



On 7/24/2022 6:19 PM, Miriam Taza wrote:


External Email - Use Caution

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

[Ariana Fei]

External Email - Use Caution

I'm attaching a list of command I used to convert freesurfer cortical
thickness output to native space:

$Caret5_Command -file-convert -fsc2c
"$FreeSurferFolder"/surf/"$hemisphere"h.thickness
"$FreeSurferFolder"/surf/"$hemisphere"h.white
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -spec-file-add
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".native.c5.spec
surface_shape_file
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret5_Command -metric-set-column-name
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
1 "$Subject"_"$Hemisphere"_Thickness
$Caret5_Command -file-convert -format-convert XML_BASE64
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -set-structure
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Structure
$Caret7_Command -add-to-spec-file
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
$Caret7_Command -metric-palette
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp
-disp-pos true -disp-neg true -disp-zero true
#cp
"$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii
#commented out GW
$Caret7_Command -add-to-spec-file
"$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure
"$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii

This already gives negative cortical thickness values in native space.

Ariana
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On Thu, Jul 28, 2022 at 12:29 PM Archibald, Jessica <
jessica.archib...@ubc.ca> wrote:

> External Email - Use Caution
>
> Hi,
>
>
>
> I signed up last night to send a freesurfer question, but I figured it
> out. Now I am getting bombarded with emails from this thread and can’t see
> a ‘unsubscribe’ button. Can you help with this??
>
>
>
> Thanks in advance,
>
> Jessica
>
>
>
> *Jessica Archibald* M.Sc.
>
> Kramer Lab- PhD candidate
>
> Experimental Medicine
>
> ICORD | Blusson Spinal Cord Center
>
> 818 W 10th Ave Vancouver, BC, Canada.
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Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

[Miriam Taza]

External Email - Use Caution

is it not these two lines?
# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cvs_version dev
if not, for the new recon-all I also have this: 
freesurfer-darwin-macOS-dev-20220328-fc008d0

How do i check the old recon all? It was done in the past.is there a log?



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

Sent: Thursday, July 28, 2022 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

What version of FS are you using for recon-all?

On 7/25/2022 9:45 PM, Miriam Taza wrote:

External Email - Use Caution

I reran sclimbic and I get the same result as the first time I ran sclimbic.
I also reran recon all on one subject. The etiv now differs from the original 
recon all and the sclimbic output (although it is closer to sclimbic).

Here is the log for both recon all.

original recon all, etiv = 1169944.199744

# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt 
--subject sub-1221084
# SegVolFileTimeStamp  2018/02/28 00:18:52

new etiv = 702243.513916
# cvs_version dev
# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats 
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/Applications/freesurfer/ASegStatsLUT.txt --subject sub-1221084
# SegVolFileTimeStamp  2022/07/25 21:04:31

sclimbic etiv= 686180.089200

>From a quick glance, the other values dont seem to differ by much between 
>recons so I'm not sure why this is happening with etiv nor what value to 
>accept.

Please let me know if there is something else I can do or if you need more info.

Miriam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Miriam Taza 

Sent: Monday, July 25, 2022 2:45 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev


External Email - Use Caution

I am getting eerror: mri_segstats: could not open atlas transform file 
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm
The results do agree when Re running sclimbic.

it seems that when etiv differs a bit from the median, sclimbic module 
calculates etiv to an extreme.
Is this expected to happen? I am concerned if my volumes are incorrect.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Sunday, July 24, 2022 10:38 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] etiv value differs if using recon all vs freesurfer 
dev

I cannot replicate this on my data. The differences are rather extreme (factors 
of 3). Can you get us access to the one with the largest difference? YOu can 
also try regenerating the aseg.stats file, eg,
cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/redo.aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject subject

Check the eTIV in redo.aseg.stats against that in aseg.stats, then re-run 
mri_sclimbic_seg to see if the results agree.


On 7/24/2022 6:19 PM, Miriam Taza wrote:

External Email - Use Caution

Hello,

I am getting different etiv values when running recon(orange) all VS 
mri_sclimbic_seg (blue). My analysis uses limbic volumes extracted from the dev 
version but I am not sure if I should just use the etiv from recon all, given 
the data is tighter (see attached). Why is there this discrepancy and what do 
you recommend?

[cid:part1.ZsO56paS.r3IDc4tc@mgh.harvard.edu]
Thank you!



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[Freesurfer] Unsubscribe?

[Archibald, Jessica]

External Email - Use Caution

Hi,

I signed up last night to send a freesurfer question, but I figured it out. Now 
I am getting bombarded with emails from this thread and can’t see a 
‘unsubscribe’ button. Can you help with this??

Thanks in advance,
Jessica

Jessica Archibald M.Sc.
Kramer Lab- PhD candidate
Experimental Medicine
ICORD | Blusson Spinal Cord Center
818 W 10th Ave Vancouver, BC, Canada.
[UBC E-mail Signature]

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Re: [Freesurfer] etiv value differs if using recon all vs freesurfer dev

[Douglas N. Greve]

What version of FS are you using for recon-all?

On 7/25/2022 9:45 PM, Miriam Taza wrote:


External Email - Use Caution

I reran sclimbic and I get the same result as the first time I ran 
sclimbic.
I also reran recon all on one subject. The etiv now differs from the 
original recon all and the sclimbic output (although it is closer to 
sclimbic).


Here is the log for both recon all.

original recon all, etiv = *1169944.199744*


# cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11
greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats
--pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent
--subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
--totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt
--subject sub-1221084
# SegVolFileTimeStamp  2018/02/28 00:18:52

new etiv = *702243.513916*
# cvs_version dev
# cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum
stats/aseg.stats --pv mri/norm.mgz --empty --brainmask
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
--excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv
--surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab
/Applications/freesurfer/ASegStatsLUT.txt --subject sub-1221084
# SegVolFileTimeStamp  2022/07/25 21:04:31

sclimbic etiv= *686180.089200
*

*
*
>From a quick glance, the other values dont seem to differ by much 
between recons so I'm not sure why this is happening with etiv nor 
what value to accept.

*
*
Please let me know if there is something else I can do or if you need 
more info.


Miriam

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Miriam Taza 


*Sent:* Monday, July 25, 2022 2:45 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs 
freesurfer dev


External Email - Use Caution

I am getting eerror: mri_segstats: could not open atlas transform file 
/export01/local/freesurfer/subjects/sub-1221084/mri/transforms/talairach.xfm

The results do agree when Re running sclimbic.

it seems that when etiv differs a bit from the median, sclimbic module 
calculates etiv to an extreme.

Is this expected to happen? I am concerned if my volumes are incorrect.



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


*Sent:* Sunday, July 24, 2022 10:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] etiv value differs if using recon all vs 
freesurfer dev
I cannot replicate this on my data. The differences are rather extreme 
(factors of 3). Can you get us access to the one with the largest 
difference? YOu can also try regenerating the aseg.stats file, eg,

cd subject/
mri_segstats --seed 1234 --seg mri/aseg.mgz --sum 
stats/redo.aseg.stats --pv mri/norm.mgz --empty --brainmask 
mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm 
--supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
--totalgray --euler --ctab 
/usr/local/freesurfer/7.2.0/ASegStatsLUT.txt --subject subject


Check the eTIV in redo.aseg.stats against that in aseg.stats, then 
re-run mri_sclimbic_seg to see if the results agree.



On 7/24/2022 6:19 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,

I am getting different etiv values when running recon(orange) all VS 
mri_sclimbic_seg (blue). My analysis uses limbic volumes extracted 
from the dev version but I am not sure if I should just use the etiv 
from recon all, given the data is tighter (see attached). Why is 
there this discrepancy and what do you recommend?



Thank you!

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Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

[Douglas N. Greve]

Have you looked at the input volume to see if there is anything strange 
about them? What kind of scans are you passing to it? What is the 
resolution?


On 7/25/2022 9:03 PM, Miriam Taza wrote:


External Email - Use Caution

Hello,
I noticed 20 out of ~240 subjects left basal forebrain volumes were 
not picked up after running ScLimbic. These are healthy adults and 
their scans look good. Also, I noticed often when this occurs NAcc is 
also 0 or other regions.
I am concerned if there is a systematic issue with left volumes ending 
up smaller than they should relative to right.


Thanks,
Miriam

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Re: [Freesurfer] FSFAST first level covariates

[Douglas N. Greve]

Yes, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation



On 7/25/2022 6:56 PM, Angela Fang wrote:


External Email - Use Caution

Hi Freesurfer community,

I have run participants through an event-related fMRI task in which 
subjects rate whether trait adjectives are descriptive of themselves 
or not, and afterwards asked them to rate each trait word on emotional 
valence. Is it possible to include these individual level subjective 
ratings of emotional valence as covariates in the first level contrast 
in FSFAST? If so, how?


Thanks,

Angela

---

Angela Fang, Ph.D.

Assistant Professor
Department of Psychology

University of Washington

Lab website: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.uwconnectlab.com 



Pronouns: she, her, hers


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Re: [Freesurfer] Cortical Thickness measures using different ways of processing

[Douglas N. Greve]

how are you converting them?

On 7/27/2022 11:20 AM, Ariana Fei wrote:


External Email - Use Caution

Hi,

We are recently trying to get cortical thickness from freesurfer and 
converting them to 32k. A problem we notice is that after converting 
to 32k, all the cortical thickness values become negative. However, 
when we load freesurfer thickness files in freeview, everything 
appears normal. We wonder if merely inverting what we currently have 
in 32k would be a good idea. Alternatively, we also calculated the 
Euclidean distance of pial and white after they have been converted 
into 32k space, which should be cortical thickness. However, when 
comparing the inverted values and the "pial-white"values, we find that 
there are some differences. In this case, has anyone ever had similar 
issues and have suggestions on which one to trust?


Thanks!

Ariana


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Re: [Freesurfer] Fwd: eTIV

[Douglas N. Greve]

I usually just divide the volume by the eTIV (you can do this in 
asegstats2table with the --etiv flag). Some people will use it as a 
nuisance regressor in the GLM


On 7/27/2022 3:11 PM, Bouchra Guelib wrote:


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-- Forwarded message -
De : *Bouchra Guelib* 
Date: mer. 27 juil. 2022 à 19:28
Subject: eTIV
To: 


I hope you can help me with this  point
I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and 
'rh.aparc.stats'. Now I want to use these measures as input data for 
my model. However, I read that we need to normalize this data using 
eTIV. Can you tell me how?


--
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com**





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[Freesurfer] The password request for the Freesurfer VirtualBox Image

[Nina Omejc]

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Hi,

My name is Nina and I'm a PhD Student from Department of Knowledge technologies At Jožef 
Stefan Institute, Ljubljana. I downloaded " Freesurfer VirtualBox Image" and I 
need the paswword
to login as the user "developer" in the login menu.

Thank you.

Best regards,

Nina
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Re: [Freesurfer] Problem with hypothalamus subunits?

[Iglesias Gonzalez, Juan E.]

Thanks for reporting this bug, Victor. I just fixed it. The fix will be 
propagated to the development version in the next couple of days but, if you 
want, you can keep using the version you’ve got by adding the flag --crop 1000  
(where 1000 is a number bigger than your image size in any dimension). That 
will have the same effect as the fix.

Cheers,

Eugenio

Juan Eugenio Iglesias
http://www.jeiglesias.com

On Jul 27, 2022, at 15:03, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
mailto:vz...@bidmc.harvard.edu>> wrote:

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Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with 
running subunits:

mri_segment_hypothalamic_subunits --s 10893/
using 1 thread
/mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: 
DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has 
a more predictable return type. To obtain get_data() behavior going forward, 
use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise  as of 
version: 5.0
  volume = np.squeeze(x.get_data())
predicting 1/1

the following problem occured when preprocessing image //0893/mri/nu.mgz :
'NoneType' object is not subscriptable
resuming program execution


segmentation  saved in://10893/mri/hypothalamic_subunits_seg.v1.mgz
volumes saved in:  //10893/mri/hypothalamic_subunits_volumes.v1.csv
resampled images saved in: 
//10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz

If you use this tool in a publication, please cite:
Automated segmentation of the hypothalamus and associated subunits in brain MRI
B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias
NeuroImage 2020



Is this a problem with tensorflow? It does not seem clear. No files are 
actually being written

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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[Freesurfer] Applying bonferroni clusterwise correction for 2spaces with PALM F-contrast

[Hye Min Shin]

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Hello experts,

I am going through FreeSurfer's repeated measures anova tutorial using
fspalm. I understand that fspalm frontend can only do t-tests at the moment
and NOT F tests as noted in this thread:
https://secure-web.cisco.com/1t11cJOK6FCdHxqm_O6WFHk15uAjWyctjoR7VAvgTW5hEaA9_sjyiYALB2fXd9m-FBh0Kg1PL3ad0gmauXJptgr0OsSWIvH5yvW90C6JcTsY4dGgSxgdJoupwln1lD4NF5DCNyY4MC94KrGS6gjEl1Ef6mnRQ8DaPW6IPC52_OSOeQ6yIFJk-pIQ_l6hU36sO0w4ltduXeRUdUWUoi76970J03S0tfYdkXYyb2NdDj1k0tZcwBlo0R-ZbSHw2T1PE1g-d7qZ_Z44hYS4u0cjJ0E-lojR-V2PxgCrMFthMVIPZorvaHSNYacIejldVs_yR/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68722.html

So I am trying to run F-contrast on PALM but I was wondering if I also have
to worry about bonferroni clusterwise correction. If I used --2spaces
option when using fspalm frontend, I thought I should also try to apply the
equivalent bonferroni correction when running F-test on FSL palm.

For the F-test on FSL palm, it looked like I could run the following
command with the addition of -f and -ftestonly flags (shown in underline):

palm -i lh.thickness.mgz -i rh.thickness.mgz -d design.mat -t design.con *-f
design.fts* -o myresults -n 2000 -corrcon -corrmod *-ftestonly*

taken from this email thread-
https://secure-web.cisco.com/1vFEFTKkUMsHsCHW3u3SsOIpxhqtkKCXdjWw6TLTufeciiVfUYjAr_XeZnYwIKAUVRX_dO9rzxwwyR9rR6mSBffHF-vk47xcYk6DDpo0bN5Vg914LJHctM8q7zowkBB5l_I6yZHOhfRsx6n8JTmTmVY6Bms3mgy1N20o6t8pg_u1hnZFtegys2UKbC4eNBHhiJL4vwbbgRN9qWob_BqGSuLcDDqWMNWy_eej8I91a1cHluQ1WnvPWNeXmN77iNJuL97H0qkQ36AGdFY35H0dzit5mMc1n5U1rdNXpLXRkzdg8TUHW0lLth6szSrfwbb4N/https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FA2%3DFSL%3B42baf4dd.1608

Would this be equivalent to the bonferroni correction methods that fspalm
uses? When I go through fspalm.log it seemed to run mri_surfcluster and
mri_segstats after running fspalm with certain commands having --sig2p-max
and --bonferroni-max 2 flags.

Thank you in advance for your help!

Best,
Julia Shin
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