[Freesurfer] lme_realizedPower

[Bernardoni, Fabio]

Dear Freesurfers,

I have used an LME model to describe the evolution of cortical thickness in a 
patient group during therapy and to compare it, at the end of the therapy, with 
an HC group. An F-test, using the lme_F function gives no significant 
difference. Now I would like to understand to which extent this means that the 
cortical thickness in the two groups is the same. Certainly this cannot be 
proven, but I believe one could conclude something like this:
"with our sample size and observed standard deviation, it there had been a 
difference say of 0.01 mm between the two groups we would have probably found 
it at a confidence level of 95%, say with a probability of 80%".
I thought the function: lme_realizedPower would help me, but I am now convinced 
it does not, because it looks to me just a one to one function of the p-value.
Is there a function that does so? What is lme_realizedPower useful for?

Thanks in advance,

Fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie

Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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[Freesurfer] freesurfer preproc output

[Bernardoni, Fabio]

Dear all,

after running a freesurfer preprocessing, in each subject subdirectory, the 
following files are produced:

lh.avg_curv  
lh.curv 
lh.curv.pial

(and the analogue for the right hemisphere)

what is the content of these files? sure, I can guess they represent the local 
curvature. but which one? the intrinsic? the extrinsic? 
what is the relation with the measures:

gauscurv, meancurv, foldind, curvind

obtained through the aparcstats2table?

It was quite surprising to me that on the wiki no precise definition is 
present, although one can guess that gauscurv is the intrinsic and meancurv the 
extrinsic curvature. what are foldind and curvind by the way? how can one get 
the intrinsic and extrinsic curvatures from the lh.curv files?

since these are all very useful measures, it would be of much help for me and 
other users (I believe) if some more intormation could be written on the wiki. 

thanks for any help,

fabio






Dr. Fabio Bernardoni
wiss. Mitarbeiter
Psychosoziale Medizin und Entwicklungsneurowissenschaften
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206
URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de
Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] how does the content of the curv files compare to that of smoothwm.H.crv

[Bernardoni, Fabio]

Dear Bruce,

thanks a lot for your answer. I am still a bit confused. I followed your 
suggestion to use msris_curvature to compute the curvature on the white surface 
(unsmoothed) instead of on smoothwm:

mris_curvature -w -a 10 $subj/surf/lh.white
mris_preproc -s $subj --target fsaverage --hemi lh --meas white.H --out 
./measures/lh.white.H.mgh
mri_surf2surf --hemi lh --s fsaverage --sval ./measures/lh.white.H.mgh --tval 
./measures/lh.white.H_sm10.mgh --fwhm-trg 10 --cortex --noreshape
(mri_surf2surf smoothing was applied also to other curvatures)

If I understood right, mris_curvature uses a hessian method to compute the 
curvature, while mris_curvature_stats uses the Gauss-Bonnet theorem (I 
extracted this information from your email to this mailing list from: Fri, 26 
Feb 2010 05:54:32 -0800). In an email from Wed, 30 Mar 2011 12:40:58 -0700, 
Rudolph says that gauss-bonnet procedure is more robust against noise. Does 
this also hold for the mean/extrinsic curvature? I ask because in the 
Gauss-Bonnet theorem only the gaussian curvature is mentioned. For the 
extrinsic/mean curvature (see attachment) I obtain that actually the 
smoothwm.H.crv seems to be the noisiest quantity (red in the histogram), 
followed by the classical method applied on the unsmoothed white matter surface 
(blu) and by the classical method applied on the smoothed wm surface (green, 
corresponds to the ?h.curv files produced by recon-all). This observation also 
holds when comparing the curvature in ?h.curv.pial and ?h.pial.H.crv (histogram 
sent in my previous email). In that case, on many vertices the mean curvature 
computed with the gauss-Bonnet method was ~1/mm which makes me think to 
unrealistically small 'hollows' on the pial surface.

Finally, to compare curvature vertexwise between a group of patients and 
controls, which should be the right numerical quantity to look at:
1- curv.pial (classic method on smoothed pial surface - from recon-all)
2- pial.H (classic method on smoothed pial surface - from mris_curvature)
3- pial.H.crv (gauss-bonnet method on the pial surface - from 
mris_curvature_stats)?


Thank you very much for any help,

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter
Psychosoziale Medizin und Entwicklungsneurowissenschaften
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206
URL http://www.uniklinikum-dresden.de/psm; www.transdenlab.de
Universitätsklinikum Carl Gustav Carus & Medizinische Fakultät
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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[Freesurfer] gyrification and longitudinal processing

[Bernardoni, Fabio]

dear freesurfer enthusiasts,

does it makes sense to compute the local Gyrification Index (lGI) on 
longitudinally preprocessed subjects?

thanks
fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206



Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113






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[Freesurfer] Problem with freeview

[Bernardoni, Fabio]

Dear all,

trying to follow the freesurfer longitudinal tutorial I encounter the following 
problem. 
Commands I digit in a new shell:

~>tcsh
~>source $FREESURFER_HOME/SetUpFreeSurfer.csh
~>setenv SUBJECTS_DIR freesurfer_tutorial/long-tutorial/
~>cd $SUBJECTS_DIR
~>freeview -f 
OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1
 --timecourse --colorscale

Output:
Option 'timecourse' not recognized. Run 'freeview -h' for more information.

1- If I remove the timecourse option together with another 3 the command 
executes correctly. 
2- As output of the bugr command I get:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-64-generic x86_64

Could anybody please telle me what's my problem?

Thanks
Fabio




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Re: [Freesurfer] Problem with freeview

[Bernardoni, Fabio]

Dear Ruopeng,

I didn't install it myself, but I guess it is a stable one. Are you suggesting 
the timecourse option might simply not be available in the stable version?

thanks
fabio
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[Freesurfer] Sniffing dialect of qdec table in asegstats2table

[Bernardoni, Fabio]

Dear all,

I am trying to perform a longitudinal lme analysis using freesurfer 5.3.0. For 
qdec tables with many columns the asegstats2table (and similarly 
aparcstats2table) commands fail with error message:

asegstats2table  --qdec-long ./qdec/long.qdec.table.dat --delimiter space 
--meas volume--stats aseg.stats  --tablefile ./measures/lme.aseg.table.txt
SUBJECTS_DIR : /sw/global/applications/freesurfer/5.3.0/x86_64/subjects
Traceback (most recent call last):
  File "/sw/global/applications/freesurfer/5.3.0/x86_64/bin/asegstats2table", 
line 514, in 
subj_listoftuples = assemble_inputs(options)
  File "/sw/global/applications/freesurfer/5.3.0/x86_64/bin/asegstats2table", 
line 316, in assemble_inputs
dialect = csv.Sniffer().sniff(f.read(1024))
  File "/home/dgeisler/env/lib/python2.7/csv.py", line 184, in sniff
raise Error, "Could not determine delimiter"
_csv.Error: Could not determine delimiter


A solution in my case is to change the line:
dialect = csv.Sniffer().sniff(f.read(1024))
to:
dialect = csv.Sniffer().sniff(f.read(2048))

Namely the snifffer needs a larger chunk of file to be able to determine the 
delimiter, in my case. However I think it would be good if one could give the 
delimiter of the infile as an option from command line. If  I have correctly 
understood the --delimiter option available so far is for the output file, 
which I called  ./measures/lme.aseg.table.txt .


Cheers,
Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie

Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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[Freesurfer] how to choose the best random effect in LME models

[Bernardoni, Fabio]

Dear Freesurfer Users,

I am trying different LME models to describe the time evolution of cortical 
thickness in anorexia patients. The LME tools provide a function (lme_mass_LR) 
to test whether a model with q+1 random effects is better (fits the data 
better) than one with q random effects, eg whether a model with random 
intercept and slope is better than one with only intercept random.

I have two questions:
1- is there a similar function to test whether the model with intercept as a 
random effect is better than the model with slope as a random effect (ie two 
models with the same number of random effects)? In another thread I read one 
should judge which random effect is to be chosen from the percentage of voxels 
where one has convergence. It sounds reasonable, but an explanation of why this 
should be so would be welcome.
2- does it make sense to use lme_mass_LR to test whether a model with 1 random 
effect is better than one with 0 random effects? I have it with something like:

LR_pval = lme_mass_LR(lhstats_0RE,lhstats_1RE,0);

And I get as a result LR_pval= 0.3 (a constant vector) which I do not know how 
to interpret: something wrong, this test does not make any sense, choose the 0 
random effect model ...

Thanks in advance for your help.

Cheers,
Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie

Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206

Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
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Re: [Freesurfer] memory allocation error

[Bernardoni, Fabio]

External Email - Use Caution

Dear Freesurfers,

when running the longitudinal preprocessing on a subject, I get the same error 
as described here (see recon-all.log attached):
https://secure-web.cisco.com/1Ip5HtCg9MqyghYHl20NFxCMImoJoShIH1y6ytQEK2tKtD13Oz0AIBueggTl_ahZFc6uNPUz7V5A3mUmh5acqtEUgyjJdjPb5JMcglhVsNmdkpAzFguuG2x10cblbsfNFAee3bxX5k-azvnAx_hKV1PE37o4wXcPwHktYZyVK41CFA6ORc_6kYF6Oeggr2XYVTNetiT3e1BLbi48zEiKnO6voUBrNf0s8ORynZS2fDVBP8_N97yBlOqXg0rHCaZ7J/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html


my FS version is:
recon-all -version
freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e

and I did not perform any editing, so there is no control points to remove as 
suggested in the above post (which also refers to version 6). Therefore, if I 
understand correctly, my problem is a different one. Any clue what I might be 
doing wrong?

Other possibly useful information:
uname -a
Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP 
Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux




Thanks for any hint/help

Fabio Bernardoni


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15HwLpU5VlSqNSJlIROcqXzy17m5cEVlxA22c1BhqN_Pd35FjWpytolF845HPS01awNT_zQjyBI2m111j6rfITVzmgLONDhN9TsY6iqtWtRw-L7GGq_-D5Xe21auR1Uzm7UWoNQc2NGcHCtRsew025Yy1KQK2P5a5dJswZWaaed3oc2q387r4yCuG7mURf_MvfjReKjdbI2w9pu3_3MKHhKojdohuGKOyNFXkFrpIeLdanqBd_Rb6Kp0vSlrh3OwJ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1jdKs38Kd-Oms54JIKsH7_jGGI6wne-La9XILjLrzWQA_NwYCrBNNiPmBWfJ_PmVPghuil6_kzbBmGRYz8u9kBxrj9uZgcJLgl1dtjtS6zamTE20CMRjpQkavy0Zfopf32rVUtTXCWjk3pX34eLI4PLF2BqkUem3ZNiNDU72mvG1Of_-ecgRdUR_5gl75hvfOkGJpDLeF_nO57s-GY3QTe02_mGjrodqxZTCYnMutvYVqku1iW77jtC1zrnXzOdlb/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQX3ciqL6MpBuoKJW4zSBsjm1-hkGi1PLKyPZE8Tcbj1pjOcrCJJkJ7qKAx5eL4RBWnLPJBAbX31xR-GlBA9FIeZDivhcuPx0hHrRUMMt4TambZSKoQKZ4iScG8Q1h4hmPSfrMq29G-B1zxH2miODaPELkxaDX1ad3onPJjTo54XUwhbPTZpw-dzwKrA4ZSl9Txu6OLhHeOAWnumjFmD/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQX3ciqL6MpBuoKJW4zSBsjm1-hkGi1PLKyPZE8Tcbj1pjOcrCJJkJ7qKAx5eL4RBWnLPJBAbX31xR-GlBA9FIeZDivhcuPx0hHrRUMMt4TambZSKoQKZ4iScG8Q1h4hmPSfrMq29G-B1zxH2miODaPELkxaDX1ad3onPJjTo54XUwhbPTZpw-dzwKrA4ZSl9Txu6OLhHeOAWnumjFmD/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


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Re: [Freesurfer] memory allocation error

[Bernardoni, Fabio]

External Email - Use Caution

Sorry I forgot the attachment.



Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: Bernardoni, Fabio
Gesendet: Dienstag, 11. Mai 2021 10:20:19
An: freesurfer mailing list
Betreff: AW: memory allocation error

Dear Freesurfers,

when running the longitudinal preprocessing on a subject, I get the same error 
as described here (see recon-all.log attached):
https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html


my FS version is:
recon-all -version
freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e

and I did not perform any editing, so there is no control points to remove as 
suggested in the above post (which also refers to version 6). Therefore, if I 
understand correctly, my problem is a different one. Any clue what I might be 
doing wrong?

Other possibly useful information:
uname -a
Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP 
Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux




Thanks for any hint/help

Fabio Bernardoni


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_za

[Freesurfer] how to visualize statistical maps in FS7.1?

[Bernardoni, Fabio]

External Email - Use Caution

Dear Freesurfers

I recently moved to FS7.1 and I was trying to reproduce my workflow I had with 
FS5.3.

To visualize statistical maps, I had always used tksurfer. It seems, however, 
it is no longer maintained. 

When I launch it it fails to find out the tix, tcl, etc libraries. Following 
this thread:
https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html

I tried to use tksurferfv.  However, when trying to overlay the sig.mgh output 
of mriglmfit, on an inflated fsaverage surface, the program shuts down, with 
this error:

freeview -f 
/usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv
 -viewport 3d
terminate called after throwing an instance of 'int'
Abort (core dumped)





What would you suggest to visualize statistical maps in FS7? Is my problem 
expected?

Thank you in advance for your attention

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhEyJg3GuHzjb7IPAU-FCiyn7epXi34kENaICaL_blhCQ8oexcOBMTiefsG3_aAP0L5sU_H9y1xYVTw6Wh6hIqLbAa4i4vAgC5EkA-lRurbVwk8nsJ2OkIW9GfadFxibvScxITahbmnRCznxGJlPF-53t2LTXrv5ovrctRRUr3HCbs6q1-FfiwpZbapsJCpLgnVMXDIXmR9FalmQ1tAveKdaDRqfq1X5OnoG5ccMFg/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_rVe8WFPk8CrMRmNwa_OuMhrKZXOFFO-FGw4FoQLrEFxfrO0Bmrs52S58GLUHqIsCPDL1IlMhZljPMxwDvqHheBhbH3FY9WwkZleNf0vOcLN7T--LeyLSKHC_sDn8owSIUefCSKVrRFaCMbFr5M04ZXYBHqA2QiHHZt1TpSnAlfoaQMAYejGip5Lnf_rIw4wUFl8P8g9z1Vi1EDDQW72FYV0DvC7gVAebazbP_AQ/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


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Re: [Freesurfer] how to visualize statistical maps in FS7.1?

[Bernardoni, Fabio]

External Email - Use Caution

Dear Greve,

thanks for your reply.
These are my steps (I corrected the second):

1) I open the inflated surface:

tksurferfv fsaverage lh inflated

(this successfully displays the inflated left hemisphere of the average subject)

2) I now load the overlay from the freeview window (sig.mgh from a mri_glmfit)

(this successfully overlays the -log(p) statistical map)

3) I would like to threshold the map using FDR<.05. This was possible in 
tksurfer:
https://secure-web.cisco.com/1Zl2C3ogXmhGUNaxqBtskesqKl5yJdBXWaIvAlRRQc78fBLhpOj_v_7pLy07rK0_Z6hz1XHxScIJY7gHTDUT17eiC8QX-MPYtvtt7GifemJKKPlDazCGKddv42OFS-Gwz2Z4fU12mu5IIXu1ZOINcKdasomLeTOTciS1_66TzuhEVpsJO_1cUjEVdrvmJkzs2aUNzN0GI8TZP6AofozZwh9xw1gvOcAB0tP8q-6-w-u5zc27Rt1QOJOHmkIRN9l_0g_L8DOdhDNfRUbn10u7wCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkSurferGuide%2FTkSurferWorkingWithData%2FTkSurferOverlay

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1YX3ipy7sscoJinbT24JROYpvfMLxUzj6WI8zTOix4cybxxCpuT0Pg_pkoLQLv7n5vAYqezvCBlC0IVATrRHdYuJ4tGGbBP7iHyIc4b54qDva92Ito4SGjZegyEvhQIz36JtilEpoZH3vbMxrYF7RZgMx_7wHkkbBj9oa41Mdk6eNPRh4TodNL1Ro8ltljQMkYFuQ-9cCs54cHXYkwpVkamTIweEnN3l7k_zjj6kQfkcl9ii4GSg485eIYx-5mpZD2Wyn3xmDyLYAGv_j9iyyyA/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1FLummlkSSdFqIQV8zg9pbFpjFgeXVHEbYHk2pa_UduhDt_bSjIPmILuhE9ffjkaYKrDBtYwuMXxg35s-lBplbWKOdhWKO6jW2yQlWTIDnZd48dpf70OWhl07hTefqn68qJ4v8ExrpOtfQhvav0_NHwz1W290JJfYWpXsuayJRZutZqcukbatksxvIABLFv-Ic6zLF06gmCN3ABzCcXsGPlhgvtslwReMK-welB7knanannNBYCEnsNHgvLC57qCTUNZq75tGHtQFFq4G8dX4KQ/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/14YWF1gwph2SJoLo23bw_XI_Fbt7k9lApqP-e0tKnEcSkhso74cT7TR0_W-2NU7zviguEOJNHbtwedhBxO4muoLSq4FlJ1SCdu057ZeaVsPfdc-gwZFcrm8fOgx00KR_ZyTgCmDaQymWKy7evJq1mY6I0NQ92ifbpMQW5MgiefhdwmaH9x_CSaoDAuFaEH6gWZmJMZsh-syBOBXW1aMR1YGOixzHN_0P94VWN-t7JJalg0SL0O01n7IEQkYOBBWKTtvJe5g9sErSKYHN-UrDrhA/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/14YWF1gwph2SJoLo23bw_XI_Fbt7k9lApqP-e0tKnEcSkhso74cT7TR0_W-2NU7zviguEOJNHbtwedhBxO4muoLSq4FlJ1SCdu057ZeaVsPfdc-gwZFcrm8fOgx00KR_ZyTgCmDaQymWKy7evJq1mY6I0NQ92ifbpMQW5MgiefhdwmaH9x_CSaoDAuFaEH6gWZmJMZsh-syBOBXW1aMR1YGOixzHN_0P94VWN-t7JJalg0SL0O01n7IEQkYOBBWKTtvJe5g9sErSKYHN-UrDrhA/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Donnerstag, 13. Mai 2021 17:11:29
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?

your tksurferfv command line is wrong

On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had 
> with FS5.3.
>
> To visualize statistical maps, I had always used tksurfer. It seems, however, 
> it is no longer maintained.
>
> When I launch it it fails to find out the tix, tcl, etc libraries. Following 
> this thread:
> https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html
>
> I tried to use tksurferfv.  However, when trying to overlay the sig.mgh 
> output of mriglmfit, on an inflated fsaverage surface, the program shuts 
> down, with this error:
>
> freeview -f 
> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv
>  -viewport 3d
> terminate called after throwing an instance of 'int'
> Abort (core dumped)
>
>
>
>
>
> What would you suggest to visualize statistical maps in FS7? Is my problem 
> expected?
>
> Thank you in advance for your attention
>
> Fabio
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & 

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

[Bernardoni, Fabio]

External Email - Use Caution

Ok I found a solution using separately mri_fdr

thanks anyway!

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: Bernardoni, Fabio
Gesendet: Freitag, 14. Mai 2021 17:28:18
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] how to visualize statistical maps in FS7.1?

Dear Greve,

thanks for your reply.
These are my steps (I corrected the second):

1) I open the inflated surface:

tksurferfv fsaverage lh inflated

(this successfully displays the inflated left hemisphere of the average subject)

2) I now load the overlay from the freeview window (sig.mgh from a mri_glmfit)

(this successfully overlays the -log(p) statistical map)

3) I would like to threshold the map using FDR<.05. This was possible in 
tksurfer:
https://secure-web.cisco.com/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7NSOhmp_YRd_jgi1SujzPXH9cIwy0Jernwep4nXrHFntFwpmUGWaIX6TS3NaUOhiQOpi-4w3nsq0bzphVsDjhFHhzNZiBY2LmWmseyLnHL2_5Ush2yKkKt5RdI2Rb74ulrrCLToWDqAnLUM0q_qlRi1RA239cuSMcBgPwpPvJtGGN411DfZewDIyQVbpNY2MLzO1iONzbuI6zyeP0zy7lFjVCoM-4HlMIAnGtBBf0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkSurferGuide%2FTkSurferWorkingWithData%2FTkSurferOverlay

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1riQaRreNdNrwH

Re: [Freesurfer] memory allocation error

[Bernardoni, Fabio]

External Email - Use Caution

dear Andrew,

I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude 
that this was the problem.


bests
fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Hoopes, Andrew 

Gesendet: Mittwoch, 19. Mai 2021 20:38:45
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error

Hi Fabio,

How much memory are you allowing for this process? You might want to just try 
increasing the limit on the slurm job to see if that works.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bernardoni, Fabio 

Date: Tuesday, May 11, 2021 at 4:22 AM
To: freesurfer mailing list 
Subject: Re: [Freesurfer] memory allocation error
External Email - Use Caution

Sorry I forgot the attachment.



Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

____
Von: Bernardon

Re: [Freesurfer] memory allocation error

[Bernardoni, Fabio]

External Email - Use Caution

dear all,

is there any progress on this issue? can I send more information to help with 
debugging? judging from the other entries of the mailing list this is not an 
issue that concerns only me.

thank you for your attention,

bests
fabio



Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1dOZP5j8XdDioY7tViTW7NqEi9mrvvba6PAbK6uv63gP7Q8bNrlLCYFkKfvXXNpcvR7MIg3L5wRfoQWO66UdM1HtJA4W7iKqfq4FhnnE9W2R2KwGDIaI7MjIpsOL5VryAdycFZZismV1CFp4rNE47COVEcaN7m-ypDnjnXobdlMmq5EirIKZSBuBmmU3BrEdMYwD-BFb3nS8AdCafRfCfvjcSJaTNtkXlb52Ab49xmqiAfSbLVpAV32A2F_b5QaItKY0wLlYGCGD0ZC1nbr_gag/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1C5zQD6S2aQEn7dMGBOKijRrWY8INlUWuanF5g6gCvX_Y1b1F-tAXUd55vvYP2ExpFYOE4G_Gf0Ujo0hS1Y2GnTUxWS4Q-Hw7ryBf9XfzTCb8akQhMElGzETBV9Y9Dx77zF8x-MJ9GUD0FyloeWVletfQc1s8UEKQ3yoaKTFfJ2V8wWshKFJa_JP1qacQoSHNmMiXI_FcftEAwml4E2oNwVLDD4wbGRONmoBUwVEiXo5dl7kMXPeg0RsJWGcPzoL3tA375bU9hNlgebAeMlJOhg/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Bernardoni, Fabio 

Gesendet: Donnerstag, 20. Mai 2021 11:17:05
An: Freesurfer support list
Betreff: Re: [Freesurfer] memory allocation error

External Email - Use Caution

dear Andrew,

I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude 
that this was the problem.


bests
fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Hoopes, Andrew 

Gesendet: Mittwoch, 19. Mai 2021 20:38:45
An: Freesurfer supp

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

[Bernardoni, Fabio]

External Email - Use Caution

dear all

even though on the official webpage it is advised to use freeview to display 
statistical maps because tksurfer is considered obsolete/not maintained in 
freesurfer 7, I am unable to reproduce the same figures, even when using 
tksurferfv.

one feature that is missing but can be reproduced using mri_fdr is FDR 
thresholding. however, it is not clear to me how to produce a decent color 
scale given a threshold computed by mri_fdr or any other means, which indicates 
the threshold.

could someone please suggest how to edit the color scale in freeview? or 
whether there is an alternative software to display the overlays/statistical 
maps produced by freesurfer?

thank you very much in advance!

fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtceMJDZRWhouZ5WGjYJWj9bwKrD2fD8s-hYFwlM9Zb7PnHApqOOdsXMN_UqKlRrAimZGaAbHyNmcB9eQc5bFAwPScLDl6teibcOsvSTEnICFgvqooR9lO2wtAQTJ5FeXCgJ_SpT53obkUl22C99Qs40AAaX_Wl-lb7XLeXtAn2E4QG0UtoS7p7UeyqVg_TLcctdVMNC-o4N0Uy1K879qlpx8J4ph1VuwogyQIlbGA/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiTnBFfpJazexQgemAFSqoGm7CBIyEnExxeRG6zWhYfzffjDt7l2n5yMtZAefgBXdkiV56cfJbXtHdHuWPQFlvInkSQIulWLx6mp6mbDfqfTojWarCOggU4inOp1-_BNPn9sKuPQxbme2JtgDgI3jrhzF1cGekZtMUl4O9mmuQgm5kH9QvITIy1-mBcFsoBz1x2MSpGocBouBWImztww-pm8hUehycRbu2-ob0_I6w/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRuqiG-X_1kQ8TK1iQT17dO0BYDk3mwMI5uwOMVyh7Q6C3RX_zAtLpzSDcnxl2q686FdPz6O_RCH2cMTW938-h5U6VP8oUS1kirsQCWWUQeImIkIv7P9eNcU8CQieJiLKt7tK--KMZoYDdnNILXhciGdXCnfdWPj4tzQ1dsStvviGy3pAqt7Yx6E1dZZ7-N6K0UT_hCph8stL0E4nrEX_jVenDNhXOgEjPbUf9Nq7Q/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRuqiG-X_1kQ8TK1iQT17dO0BYDk3mwMI5uwOMVyh7Q6C3RX_zAtLpzSDcnxl2q686FdPz6O_RCH2cMTW938-h5U6VP8oUS1kirsQCWWUQeImIkIv7P9eNcU8CQieJiLKt7tK--KMZoYDdnNILXhciGdXCnfdWPj4tzQ1dsStvviGy3pAqt7Yx6E1dZZ7-N6K0UT_hCph8stL0E4nrEX_jVenDNhXOgEjPbUf9Nq7Q/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Bernardoni, Fabio 

Gesendet: Freitag, 14. Mai 2021 17:35:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?

External Email - Use Caution

Ok I found a solution using separately mri_fdr

thanks anyway!

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
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http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6siv

[Freesurfer] problem with mris_compute_lgi

[Bernardoni, Fabio]

External Email - Use Caution

Dear FS experts,

when running mris_compute_lgi, the make_outer_surface step produces an error:

>> reading filled volume...
/bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp81860215899812157.load_mgh.m.mgh for reading

Looking more closer at what produces the error, it is the MRIread function:

vol=MRIread('/surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz')
/bin/bash: /scratch/tp81861321896965219.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp81861321896965219.load_mgh.m.mgh for reading
ERROR: loading /surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz as MGH

vol =

 []


I do not understand where the /scratch/tp81861321896965219.load_mgh.m.mgh is 
created/located. Is it within the rh.pial.filled.mgz? Even going through the 
MRIread function I couldn't figure out. Maybe the error is actually in the 
mri_fill step (that however exits with no error)

Thanks in advance for any hint

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1j3t_3Y4iFjkXouNEHQLd1euJWlTzdWEoUG3WoZLDjonBHv-KC04b7EqMEFAWM6bEAmyZN0IafZm8SgPcMYm43qeyeXA4CYElHMpK89qLgXTNS-MQpG4H1WfpBcdxiNKqBr49CFP89JJi4Gtf5uHkwMLMEpKN_3k3vvn6uOxKqxhZJX9fzQNqyogMHYRz-PMiNwBiiVG_fUJL1Ul0nXv7o8Sr4vcojTAOci8RL3rCR_w_8iCgkX3bXB0gb-oP3QhF/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1uAkOO7CtOzygpinM5tt9ZZHkhl_HV3HHZnI2wodEWKz8oNE1Y8bMnmCGBXt6F84SHWDhazmLk1mUGMAJABTUzGRAikxjiRElPVtx7QgBCQZi7_QAQpjILl3qi7rTZXwMLCY1PUT6XgKVGtIu7rxtTB0oGeaPes-lP5exBt8u8vNagtSKDKsd13NfA7nkwes1NiGb3G3CgF8gUZB9x7uXox-xI0OfScQpicSCmeMBV4O_Y0Dpecahs3iPsS0gPokazpqM2kxOd93GP6gFRjDSuA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
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an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1GIWqSkZNuXf_zg2CrESTkx8X0PW_gl1iao4QNgyhxPTCr3ZL5J71TSbomlWf7Vy722LMZLcaKu37Y6DpAJj59r-v1fJwe86US5FvwPWVjizzB87BvqB0O6BixNXiqYBZmb8f6rAlj-3FeyYr8KFHgvNlFnwZz8t9WQ_sh0NLiBTM8o8Mr580kDzMeDrjbfRqNcSxVZytpDkyQPMOvWjeaKxZ_GiXcsFxJlThFJGO5QKDQxaTGojFHiVPumCoJ6YsYEOKPHdJJtU59rEqGOVWKQ/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
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Re: [Freesurfer] problem with mris_compute_lgi

[Bernardoni, Fabio]

External Email - Use Caution

Dear all

I solved this. In case it is useful for someone else:

the load_mgh needs a temp dir in case the input is a mgz, to store the unzipped 
file.

To set the tmp dir, set the TMPDIR or TEMPDIR evnironment variable, otherwise 
/scratch is used if present. But in my case is not writable, so the command 
fails.

Bests,

Fabio



Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1ItIv-jpXPnKALveycIN_yCP1Wp9_oFtdN4jy1RIHA83-o31Cy2mSJcT8M2S_q4dp_Z8oRNm-hENpAVwD_qRb5u6GkiytWak4YPXaHwUqtDPZ61l0RBBGgb9E066DMid2u6Ev2-6blo1DUf0OEXna4dhXN-z1IQrs4UzpHPckiAldJJSBBqCkAEuJmto2MIm3ktiJIZoyeiu7FZt0STZftOf_SpbB-nL_ZP1ojAwMVyJh7wPF55f1VnNZaBJJwXgi/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1YdALusv0t23JR3fYBLLwG3oCI0mqdrqdgc2lSNI9nb8_fmAMEBd78xbijVAGXDBUdUd6NXr-dyxmcTtLcql_WoOGpajUNtthF5wQ5iIoaBAOlWgAuJLZ85_S3AWiLuzAqNlIOuh9OJHq3JEpvz5BP-0aFnTy2_Nmx5o-F65qpT50CJofnAcl2acjX7LJpG2IdQo_0PON-rlnrFH7CJXD45cVseetAT4dHZMbUdNPnTSvCNjgsgBf9UdKBOsH86kB1L-bKqZc2Upyyxb-NoVm7A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
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an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
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Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1PrHoaa5WUgaOOBPnzVAQS0WI8U9TsSL1jud9E_uaAs-u_NwNRGdyunfE9oIRiWgCmOdSkmWmcOBElEuHoI1D4c-_JiK33GiJYlD3OWX8vgJdWm7nZqtCl2_9NGF_KCMygtLvcOVZHI4x6sEOPSijrIULIcKGegp00B11iXSVYUl6zI-D0y8rOzZYJmsm26NYHh8bI9zP55ZQnqPDt7DDeJNH8Qus4d8piYdjxp3fma7TEVF1KyjdhYaPlNoXBX9I87xb2XeEx4iRZu8TyrdemQ/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Bernardoni, Fabio 

Gesendet: Mittwoch, 30. Juni 2021 14:07:34
An: freesurfer mailing list
Betreff: [Freesurfer] problem with mris_compute_lgi

External Email - Use Caution

Dear FS experts,

when running mris_compute_lgi, the make_outer_surface step produces an error:

>> reading filled volume...
/bin/bash: /scratch/tp81860215899812157.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp81860215899812157.load_mgh.m.mgh for reading

Looking more closer at what produces the error, it is the MRIread function:

vol=MRIread('/surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz')
/bin/bash: /scratch/tp81861321896965219.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp81861321896965219.load_mgh.m.mgh for reading
ERROR: loading /surf/tmp-mris_compute_lgi-rh.pial/rh.pial.filled.mgz as MGH

vol =

 []


I do not understand where the /scratch/tp81861321896965219.load_mgh.m.mgh is 
created/located. Is it within the rh.pial.filled.mgz? Even going through the 
MRIread function I couldn't figure out. Maybe the error is actually in the 
mri_fill step (that however exits with no error)

Thanks in advance for any hint

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1j3t_3Y4iFjkXouNEHQLd1euJWlTzdWEoUG3WoZLDjonBHv-KC04b7EqMEFAWM6bEAmyZN0IafZm8SgPcMYm43qeyeXA4CYElHMpK89qLgXTNS-MQpG4H1WfpBcdxiNKqBr49CFP89JJi4Gtf5uHkwMLMEpKN_3k3vvn6uOxKqxhZJX9fzQNqyogMHYRz-PMiNwBiiVG_fUJL1Ul0nXv7o8Sr4vcojTAOci8RL3rCR_w_8iCgkX3bXB0gb-oP3QhF/http%3A%2F%2Fwww.transdenlab.de%2F;
 
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+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
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[Freesurfer] lGI value aberrantly high, again

[Bernardoni, Fabio]

External Email - Use Caution

Dear all

as some other posted before me, sometimes the computation of lGI fails with the 
message 
(see for example: 
https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,
 
https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,
 
https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html)

'lGI for vertex number 35901 of the outer mesh is 2.5958
... remeasuring lGI value for vertex iV = 36001. It may take a few minutes.
WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high 
(lGI=53.1127)...
...lGI computation will be stopped. This may be caused by topological defects, 
check mris_euler_number on the pial surface.'

as many reported before me, computation of euler number gives 2, i.e. nothing 
wrong. another suggestion by marie schaer is to 
rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the 
-randomness option. 

The point is that the -randomness option seems to have no effect, the error 
occurs again in exactly the same place, with the exact same value 
(lGI=53.1127). 

I am using freesurfer 7.1. Has there been any development to solve this? 

Thank you in advance

Fabio Bernardoni


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQq65obryki5fZ9inqQJGhUQCH12N3Pt0ACl5Sz6LbLbSEiQUG8WQO9t88xjEbBwfnJl5zMPv5YGf2um_2huADEEKMstPPgZ-2NbXimHQPHK5qCSvFMpSsGruW0svSkAaRlYlbli_Lh272QlD4J26lfLiQzwTVCqVKRna8BCUGR8yVWddr_LDg_XEqia5dNbzYZDkwnUBTG2F9ISpoIXh3TOciVMBbhbfFjq4oyGcs3f8IYSIi2hIbnpM9C-K7UBqfq6JgC8MOXudQm7m45/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ38YRbvIQam95p0_9OaNAtoH0qHBY20t69GRnCZNTRBEMY7L0dD_0kA9XSvn1emw5Cg068ZJTAc2rajYXBSywtHWwSBJv5Bk3AMNCwDT208lNW5A1KBEHxU6ClKWG0biFGmUlIMeH8DzBxdhTFSc46EnzdD9atOQtFO8_qTgvGgNFOhfvwKS67YeTzV4Q22C-y953EVIfJo84NUaLXgIRwlO-_erSBNdJlV-6iBgXbIA2PkyekWYcjKAGknDwCZ9FeDCXXrfPaTjhOLpleBfcBwLPTaoDD3w_UZqZxxZw/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


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Re: [Freesurfer] lGI value aberrantly high, again

[Bernardoni, Fabio]

External Email - Use Caution

dear douglas

thanks for your answer. I understand the developer is not maintaining the 
program computing lGI. however, my question refers ultimately to the recon-all 
preprocessing. I am trying to make it run again using different random seed, 
but apparently it uses the same random seed. or am I wrong? whether this rerun 
with a new random seed solves the lGI problem is yet to be proven.

thanks

fabio

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM90KVg1F580Ru3Y546PmS-h-yp2hhRc5_K7k433uq2EJ9eaN9s8N9_CsTS54vv8mPbTTC2nPXc9xuueUufUXY3wMTbe-X_hCg0_ZeY_3dPgUiI9Z8XB_Gj9VNMxWl_xWy1cJLx0YYY58z5B_NtHWLg0JcHnV3Bii40hBJXokL86POx5de5HjDYxX4xjuGmgmKVcOu7L97BLr6q4WUSuF41E4SlFTBFZ6U2Tm1xn9izIPo9PZQTv9aJG7uBQpIMI0PKO3sNOOljdWZHt7nV5/http%3A%2F%2Fwww.transdenlab.de%2F;
 
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Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Mittwoch, 26. Januar 2022 23:02:04
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] lGI value aberrantly high, again

Sorry, the developer of this program has moved on in her career so we
have no one to support it anymore. We maybe looking at it again in the
next year or so.

On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear all
>
> as some other posted before me, sometimes the computation of lGI fails with 
> the message
> (see for example: 
> https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html)
>
> 'lGI for vertex number 35901 of the outer mesh is 2.5958
> ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes.
> WARNING -- Problem for vertex

[Freesurfer] volume differences between longitudinal and crosssectional preprocessing

[Bernardoni, Fabio]

External Email - Use Caution

dear freesurfer experts

comparing the results of longitudinal vs. crosssectional preprocessing for 
single time point participants I have noticed that there are some quite 
substantial differences (>5% for some sub cortical regions). I wonder whether 
this is normal, or whether I should suspect that I am using some wrong setting. 
the differences are there both when using freesurfer 5.3 and freesurfer 7.1.


I have always used the flag: -nuintensitycor-3T (our scanner is a 3 Tesla one)


I would say that I more often have smaller volumes in the longi preprocessing 
(80% of the cases), but I haven't checked this systematically.

This are the first 5 regions from the aseg.stats file:

FS5 CROSS
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1   4  4772 4772.4  Left-Lateral-Ventricle45.4073
12.814624.92.68.
  2   5   133  132.6  Left-Inf-Lat-Vent 51.9800
10.279928.77.49.
  3   7 1348813488.1  Left-Cerebellum-White-Matter  91.1006 
5.241937.   106.69.
  4   8 5756257561.8  Left-Cerebellum-Cortex72.0094 
8.703324.96.72.
  5  10  8428 8428.3  Left-Thalamus-Proper  94.7674 
7.111052.   111.59.

FS5 LONGI

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1   4  4542 4541.9  Left-Lateral-Ventricle42.8623
13.558222.94.72.
  2   5   131  130.5  Left-Inf-Lat-Vent 50.6667
11.181223.81.58.
  3   7 1357613576.1  Left-Cerebellum-White-Matter  86.1990 
4.516140.   100.60.
  4   8 5761557614.7  Left-Cerebellum-Cortex68.7623 
8.620617.92.75.
  5  10  8658 8658.2  Left-Thalamus-Proper  91.2531 
6.737452.   107.55.

FS7 CROSS

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1   4  4871 5297.0  Left-Lateral-Ventricle43.9799
11.886824.91.67.
  2   5   145  202.9  Left-Inf-Lat-Vent 53.7310
10.000928.79.51.
  3   7 1470315351.7  Left-Cerebellum-White-Matter  86.7391 
5.509735.   100.65.
  4   8 5769457174.0  Left-Cerebellum-Cortex68.6875 
9.032029.95.66.
  5  10  8674 8354.1  Left-Thalamus 89.9416 
8.136940.   107.67.


FS7 longi


# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1   4  4898 5154.3  Left-Lateral-Ventricle41.0488
12.030922.79.57.
  2   5   165  214.4  Left-Inf-Lat-Vent 52.3939
11.268727.84.57.
  3   7 1465515364.2  Left-Cerebellum-White-Matter  83.1088 
4.950939.98.59.
  4   8 5875958163.3  Left-Cerebellum-Cortex65.8093 
8.726925.90.65.
  5  10  8757 8542.9  Left-Thalamus 85.7984 
6.882147.   102.55.




thanks for any hint, and of course please let me know in case I should provide 
more informations!


fabio bernardoni


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1agu0o6sn74nWpsbJ7svbMRxn_ehBHd-f92Wr82FruYql6-5gzPLns-0KWG220DmGx-h5cqZZOWM1rIy0oPKilcVolnjxjTkTA4znrqnXz3a3mW3vf3fBrSmnMtizh16SThuPcwb0hTS3pL3O26VDQ2455LzCnYgmPZCCms5DuDfaof8UIBvWEpY7I4doWst_ks5hNagDpbfec7nPxSo2actD3cuMPxfOsJ_9nGaQjAjcfHlwxVyydCZwc04OKLZMvQRYHjVHciPPwbK571HOQpAcjSvzvuOf3EOTgOR1mttvP81BSgR5zB-w5jyn8KKM/http%3A%2F%2Fwww.transdenlab.de%2F;
 
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Re: [Freesurfer] volume differences between longitudinal and crosssectional preprocessing

[Bernardoni, Fabio]

External Email - Use Caution

dear douglas,

you are right a visual comparison is the thing to do. I hope I can ask you an 
advice on that.

I used freeview to open the mri data + segmentation for both participants:

freeview -v  $subj/mri/brainmask.mgz 
$subj/mri/aseg.mgz:colormap=lut:opacity=0.2  $subjlongi/mri/brainmask.mgz  
$subjlongi/mri/aseg.mgz:colormap=lut:opacity=0.9  &

once they are open I can play with the opacity and visualize the differences. 

my problem is that the brainmasks are shifted wrt each other. when I try to fix 
this setting the MNI305 coordinates to be the same, it does not work, it is set 
in such a way that the TkregRAS/RAS coordinates are the same. how can I change 
that?

until I fix this, I can't tell because I see differences in the snapshots I see 
but they are due to the fact I am looking at different slices of the brain...

or is this already indicative I did something wrong in the longi preproc 
because the brainmasks should be the same?

thanks a lot

fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
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+49 (0351) 458-5245
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an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
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Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 12. September 2022 16:14
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] volume differences between longitudinal and 
crosssectional preprocessing

What you show for the lateral ventricle is not really concerning to me. 
Oftentimes there are differences on border voxels, and border voxels can easily 
make 5% or more of a structure. If you compare them visually, do you see big 
differences?

On 9/12/2022 7:41 AM, Bernardoni, Fabio wrote:

External Email - Use Caution

dear freesurfer experts

comparing the results of longitudinal vs. crosssectional preprocessing for 
single time point participants I have noticed that there are some quite 
substantial differences (>5% for some sub cortical regions). I wonder whether 
this is normal, or whether I should suspect that I am using some wrong setting. 
the differences are there both when using freesurfer 5.3 and freesurfer 7.1.


I have always used the flag: -nuintensitycor-3T (our scanner is a 3 Tesla one)


I would say that I more often have smaller volumes in the longi preprocessing 
(80% of the cases), but I haven't checked this systematically.

This are the first 5 regions from the aseg.stats file:

FS5 CROSS
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName normMean normStdDev 
normMin normMax normRange
  1   4  4772 4772.4  Left-Lateral-Ventricle45.4073
12.814624.92.68.
  2   5   133  132.6  Left-Inf-Lat-Vent 51.9800
10.279928.77.49.
  3   7 1348813488.1  Left-Ce