Re: [Freesurfer] Cortical Thickness Extraction

[Bunting, Emma]

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Hi Doug,

Why should we not scale the thickness by the ICV? This is what we had thought 
to be the norm based on the literature,

How would you advise normalising these values instead?

Best wishes,

Emma

Greve, Douglas 
N.,Ph.D.<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Greve%2C+Douglas+N.%2CPh.D.%22>
 Mon, 18 Mar 2019 07:56:18 
-0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190318>

They do not have any normalization applied. BTW, you should not scale the

thickness by the ICV



On 3/18/19 10:24 AM, Bunting, Emma wrote:



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Hi Freesurfer experts,



I used a script created by ENIGMA to extract the cortical thickness values for

129 subjects that had undergone reconall processing.





We are using these values in VBM analysis. From reading other papers, we notice

that all regional volumes are usually normalised by dividing by total

intracranial volumes for each subject.







I’m just wondering whether the values we are extracting from our freesurfer

output files have already had this normalisation applied?



The script we’ve used as follows:





#!/bin/bash



echo

'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'

 > CorticalMeasuresENIGMA_ThickAvg.csv

echo

'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'

 > CorticalMeasuresENIGMA_SurfAvg.csv



for subj_id in 

[Freesurfer] Atlas Labelling on Registered images

[Bunting, Emma]

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Hi Freesurfer experts,

Does reconall register each T1 to fsaverage space?

And if yes, are the Desikan-Killany and Destrieux atlas labels still applicable?

I am asking because I noticed that when I overlayed the Desikan-Killany atlas 
onto our reconall outputs they didn’t seem to align properly,

Thanks,

Emma

Sent from Mail for Windows 10

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[Freesurfer] Cortical Thickness Extraction

[Bunting, Emma]

External Email - Use Caution

Hi Freesurfer experts,

I used a script created by ENIGMA to extract the cortical thickness values for 
129 subjects that had undergone reconall processing.


We are using these values in VBM analysis. From reading other papers, we notice 
that all regional volumes are usually normalised by dividing by total 
intracranial volumes for each subject.



I’m just wondering whether the values we are extracting from our freesurfer 
output files have already had this normalisation applied?

The script we’ve used as follows:


#!/bin/bash

echo 
'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_ThickAvg.csv
echo 
'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_SurfAvg.csv

for subj_id in $(ls -d Subj*); do #may need to change this so that it selects 
subjects with FS output

printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv
printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv

for side in lh.aparc.stats rh.aparc.stats; do

for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal 
fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital 
lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal 
paracentral parsopercularis parsorbitalis parstriangularis pericalcarine 
postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate 
rostralmiddlefrontal superiorfrontal superiorparietal su

[Freesurfer] mris_preproc calling on incorrect target surface

[Bunting, Emma]

External Email - Use Caution

Hi Freesurfer Pros,



I'm trying to perform mris_preproc with an average subject that I created 
called 'avgsubject.Patients_EB', as my target.



Although it appears to take avgsubject.Patients_EB as the target subject, and 
VIPD_010 (the first subject in my fsgd file) as the source subject, it then 
somehow swaps the target and source surfaces (sphere.reg's) it is trying to 
call upon. I am therefore getting an error because there is no 
avgsubject.Patients_EB.sphere.reg file within the VIPD_010 subject folder.



The commands I use for the mri_preproc are below, with the sections I am 
referring to highlighted in bold.

ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd 
PDonly_Liu_EB.fsgd \

> --target avgsubject.Patients_EB \

> --hemi lh \

> --meas thickness \

> --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh \

>

nsubjects = 97

tmpdir is ./tmp.mris_preproc.12493

/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer

Log file is lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mris_preproc.log

Tue Feb 12 11:20:49 GMT 2019

setenv SUBJECTS_DIR 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer

cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer

/var/drc/software/64bit/freesurfer-6.0.0//bin/mris_preproc --fsgd 
PDonly_Liu_EB.fsgd --target avgsubject.Patients_EB --hemi lh --meas thickness 
--out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh



Linux img-140.drc.ion.ucl.ac.uk 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 
18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux

$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

tmpdir is ./tmp.mris_preproc.12493

Src lh avgsubject.Patients_EB.sphere.reg

Trg lh sphere.reg









---

#@# 1/97 VIPD_010 Tue Feb 12 11:20:49 GMT 2019 --

---

mri_surf2surf --srcsubject VIPD_010 --srchemi lh --srcsurfreg 
avgsubject.Patients_EB.sphere.reg --trgsubject avgsubject.Patients_EB --trghemi 
lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.12493/VIPD_010.1.mgh 
--sval 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness
 --sfmt curv --noreshape --cortex

MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg):
 could not open file

Source registration surface changed to avgsubject.Patients_EB.sphere.reg

Target registration surface changed to sphere.reg



$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $



setenv SUBJECTS_DIR 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer

cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer

mri_surf2surf --srcsubject VIPD_010 --srchemi lh --srcsurfreg 
avgsubject.Patients_EB.sphere.reg --trgsubject avgsubject.Patients_EB --trghemi 
lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.12493/VIPD_010.1.mgh 
--sval 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness
 --sfmt curv --noreshape --cortex



sysname  Linux

hostname img-140.drc.ion.ucl.ac.uk

machine  x86_64

user ebunting

srcsubject = VIPD_010

srcval = 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness

srctype= curv

trgsubject = avgsubject.Patients_EB

trgval = ./tmp.mris_preproc.12493/VIPD_010.1.mgh

trgtype=

srcsurfreg = avgsubject.Patients_EB.sphere.reg

trgsurfreg = sphere.reg

srchemi= lh

trghemi= lh

frame  = 0

fwhm-in= 0

fwhm-out   = 0

label-src  = lh.cortex.label

label-trg  = lh.cortex.label

OKToRevFaceOrder  = 1

UseDualHemi = 0

Reading source surface reg 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg

No such file or directory

mri_surf2surf: could not read surface 
/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg

No such file or directory



n.b. that the lh.avgsubject.Patients_EB.sphere.reg file can be found within the 
avgsubject.Patients_EB/surf folder, so I believe this is an issue of simply 
mixing the target and source surfaces.



It is also worth noting that I have found your bug fix for the 
make_average_surface script, which now completes without errors. However, the 
make_average_subject script still completes with errors, and when I try to use 
the average_surface output as my target I get the same errors.



Please let me know if there is something I am doing wrong here, or if there is 
a way to fix the error I am getting!


Many thanks,


Emma Bunting

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[Freesurfer] Double cursors when viewing inflated surfaces

[Bunting, Emma]

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Hi, 

When I load my surface overlay (sig.mgh output file from GLM analysis) onto fs 
average lh inflated surface, I see two cursors when looking at the inner side 
of the brain. When i click the outer side, only one cursor shows. 

I have used this command to visualise the data: freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:anot_outline=1:overlay=glmdir/matrix/sig.mgh:overlay_threshold=4,5
 -viewport 3d

I’ve worried that the labels its loading onto the brain aren'’t aligning 
properly if the cursor is in 2 places. 

Is there something wrong with my data visualisation command?

Thanks in advance, 

Best wishes, 

Emma 

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[Freesurfer] Tutorial Data Set - Won't Download

[Bunting, Emma]

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Hello FreeSurfer Developers,

I'm attempting to download the tutorial dataset, as described on the FreeSurfer 
Tutorial Datasets page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data).

It is able to download majority of the buckner_data files, up to: 
tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/073/surf/lh.pial
, but then an error message occurs, and the download stops.

The error message reads…
gzip: stdin: unexpected end of file
tar: Unexpected E0F in archive
tar: Unexpected E0F in archive
tar: Error is not recoverable: exiting now

I have tried downloading it on both windows and linux machines.

Does anyone have any thoughts on how to trouble-shoot this one? I have a copy 
of the recon-all.log upon request if you think it will be of any use,

n.b. version of freesurfer: 
freesurfer-LInux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

Best Wishes,

Emma
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