[Freesurfer] Undo_Edits_After Saving

Hej, I was wondering if it is possible to open already edited scans and then remove some of the voxels which previously has been edited (fx. at the pial surface). While editing you can offcourse undo, but i am thinking of after editing and closing the program. Best Kasper -- Kasper Jessen

[Freesurfer] Undo manual edits to brainmask.mgz

start over with alle the edits i have done? Best regards, Kasper -- Kasper Jessen, Læge, klinisk assistent Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kaspe...@cnsr.dk eller kasper.jes...@

Re: [Freesurfer] erroneous cortical surface models

/neuropsychopharma/experimental.html > < > http://www.dppp.uzh.ch/research/psychiatric/neuropsychopharma/experimental.html > > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > ht

[Freesurfer] Controls points not transferred to [LONG]

-stable-pub-v5.3.0 Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If

[Freesurfer] Univariate_Algorithm does not converge after 50 iterations!!!

Dear FreeSurfer group, I am running the univariate analysis to test if there is a change in thickness between two groups over time. The dataset has a baseline and a follow-up scan (i.e., two time points) and consist of about 40 patients and 40 controls. I receive an an error which states "Algor

[Freesurfer] Volumes differ in acquisition paramaters

* What do the above errors mean and is it something we should be worried about? Best regards, Kasper Jessen MD, PhD Student ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The i

[Freesurfer] Recon-all variations and 3T flag

- Does it matter where you place the 3T flag in the command line? fx - recon-all -i -subjid -3T -all Best regards, Kasper Jessen MD, PhD student ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] Volumes differ in acquisition paramaters

managed? Is it possible to run freesurfer directly from the PAR/REC file? - Is the “Image geometries differ across time” related to the difference in acquisition parameters mentioned in the warning? Best regards Kasper Jessen 2015-10-10 16:12 GMT+02:00 Bruce Fischl : > Hi Kasper > >

[Freesurfer] autorecon2 vs autorecon2-cp

Phd Student -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kaspe...@cnsr.dk eller kasper.jes...@regionh.dk ___ Freesurfer

[Freesurfer] Timepoints and Analysis

using two timepoints, do you still recommend to include all the 5 time points in creating the [BASE] even though only 2 time points will be used? Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Mac Version and Output differs

:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 *iMac: * build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Best regards, Kasper Jessen

[Freesurfer] 3T or nuintensitycor3t

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej

Re: [Freesurfer] 3T or nuintensitycor3t

irach stage. > > Best, > Lee > > > On Fri, 6 Nov 2015, Kasper Jessen wrote: > > Dear freesurfer, >> To clear up som confusion i would like to ask if there is a difference >> between adding a -3T or -nuintensitycor3t flag? >> >> Best regards, >> Kaspe

[Freesurfer] Data differ depending on OSX version

is on the iMac 2.472 and on the MacPro 2.537. Is it because of a randomization generator in FreeSurfer? Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Data differ depending on OSX version

Thank you for your reply. Okay - so if i understand it correctly, then both the OS version and the computer system (i.e processor) has to be the same. What is the reason for the processer has to be the same? Best regards, Kasper Jessen 2016-01-04 15:31 GMT+01:00 Martin Reuter : > Hi Kas

[Freesurfer] Fsaverage

Dear FreeSurfer experts, In regard to fsaverage, we are wondering whether it is recommended to use the default fsaverage or if a new fsaverage should be created for the individual dataset. If there are no recommendations, what are the advantages and disadvantages? Best regards, Kasper Jessen MD

[Freesurfer] Cross sectional analysis of a longitudinal data

onal group analysis in QDEC? Best regards, Kasper Jessen MD, PhD student ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

rectories are located). > 2. yes (fsaverage should be linked there anyway, right?) > 3. yes > > ;-) Martin > > > On 03/09/2016 03:42 PM, Kasper Jessen wrote: > > Dear FreeSurfer experts, > > We have a longitudinal study design with up to 5 time points. However, we >

[Freesurfer] Matlabpool has been removed

xperienced the same. Unfortunately i cannot find the answer, which fixes the problem. As far as i understand, it may be because i am using a new version of Matlab. However, is there a way to fix the problem? Best regards, Kasper Jessen MD, PhD student ___

Re: [Freesurfer] Matlabpool has been removed

try it with that version. > > Cheers, Clara > > - Ursprüngliche Mail ----- > Von: "Kasper Jessen" > An: "Freesurfer support list" > Gesendet: Mittwoch, 23. März 2016 09:41:51 > Betreff: [Freesurfer] Matlabpool has been removed > > Dear FreeSurfer

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

cally create the ..long.. names internally). > > cheers, Martin > > > > On 03/11/2016 08:51 AM, Kasper Jessen wrote: > > Hi Martin, > > Thanks for the answer :-) > > To presmooth the data onto target, with the following command: > > recon-all -long -qcach

Re: [Freesurfer] 3T or nuintensitycor3t

turned > on using the -nuintensitycor3t flag. The -nuintensitycor3t flag only > changes the NU intensity correction parameters, without using the 3T atlas > in the earlier Talairach stage. > > Best, > Lee > > > On Fri, 6 Nov 2015, Kasper Jessen wrote: > > Dear fre

[Freesurfer] Big ventricles and recon-all error

Dear FreeSurfer group, I am having problems with a subject with very large ventricles. The recon-all exits with errors. Is it known issue that FreeSurfer is having difficulties with large ventricles? How can i solve this problem? I have read in another post, that the flag -bigventricles may sol

[Freesurfer] 3T flag

Dear FreeSurfer group, Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment. However, where can i find the documentation for the abo

[Freesurfer] T2pial and [LONG]

v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface. Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces? Best regards, Kasper Jessen

Re: [Freesurfer] T2pial and [LONG]

7;t done this yet I don't think, so there > may be undiscovered bugs. > Bruce > On Fri, 13 May 2016, Kasper Jessen wrote: > > Dear FreeSurfer, > Currently, we have only manual edited the BASE (the CROSS was left > unedited) > in an longitudinal data. However, some corti

Re: [Freesurfer] Big ventricles and recon-all error

Hi Kasper > > you might try downloading dev and see if it works. The upcoming (but never > quite ready) V6 should have much better handling of enlarged ventricles. > > cheers > Bruce > > On Tue, 10 May 2016, Kasper Jessen wrote: > > Dear FreeSurfer group, >> I am h

Re: [Freesurfer] 3T flag

I would like to know the following: a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas? b) what does the 3T-specific NU intensity correction parameters do differently than the standard? Best Kasper 2016-05-10 8:09 GMT+02:00 Kasper Jessen : > Dear FreeSur

Re: [Freesurfer] 3T flag

it that is probably wrong? Best regards, Kasper 2016-05-17 14:48 GMT+02:00 Moeller, Sebastian < sebastian.moell...@rwth-aachen.de>: > Hi Kasper, > > > > On May 17, 2016, at 10:05 , Kasper Jessen wrote: > > > > I would like to know the following: > > &g

Re: [Freesurfer] T2pial and [LONG]

> > On 05/17/2016 03:54 AM, Kasper Jessen wrote: > > Unfortunately i do not think it works to pass it directly into a > longitudinal run. I tried the following, which exited with errors: > > recon-all -long d256a d256_base -FLAIR path/flair.nii.gz -autorecon3 > -FLAIRpial &g

Re: [Freesurfer] 3T flag

dence of T1 > > Hopefully somone else can answer b) as I don't remember. > > cheers > Bruce > > > > On Tue, 17 May 2016, Kasper Jessen wrote: > > I would like to know the following: >> a) what is the differences between the 3T Atlas (schwartz atlas) and the >>

[Freesurfer] Linear Mixed Effects model

Dear FreeSurfer, I have a longitudinal study (patients and controls) with two time points (i.e., baseline and six-weeks follow-up). I would like to use the LME model as it can handle unequal timing and different number of time points across subjects due to missing data. I would like to test if t

[Freesurfer] mri_glmfit long_stats_slopes with group

Dear Freesurfer, I would like to test if the percentage change (two time points) of cortical thickness is different between two groups. What i have done: FIRST: long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-spc --generic-ti

[Freesurfer] problem with fsgd glmfit

Dear FreeSurfer, I would like to do the long. two stage model (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Study design: 2 groups (one control group, one patient group) with gender and age as covariates. Each subject was MRI scanned at baseline and 6 weeks follow-up. I

Re: [Freesurfer] problem with fsgd glmfit

I have found the reason for the error: FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input The class should be 1.0 and 0.0, as stated in the fsgd file. Otherwise, is the process still correct? BW Kasper > Original Message > Subject: problem

Re: [Freesurfer] mri_glmfit long_stats_slopes with group

Dear FreeSurfer I have read through a similar question/answer (again): http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53238.html However, i still done seem to understand how to exactly pass the output of long_stats_slopes into the following command with a C and fsgd file?? mri_g

Re: [Freesurfer] SPC in surface area

What is the unit of the spc, which you extract? Fx. in my data I have a -0.49 = does that mean a -0.49 % decrease? BW Kasper Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Martin Reuter Sendt: 19. juli 2017 11:37 Til: Freesurfer support l

[Freesurfer] longitudinal generic-time and spc

Dear Freesurfer, The following is a follow-up, on a previous discussion (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51582.html) but i am still left with some uncertain and unanswered questions. My design: Patients and Controls, MRI scanned at baseline and after 6 weeks (only

[Freesurfer] Curvature in FreeSurfer

Dear FreeSurfer, We have been discussing the mean curvature provided by FreeSurfer software. As i understand the mean curvature is measured as 1/r and has a unit of 1/mm. But a) What is the curvature an expression of? Is it the degree of folding of the brain and is it the white matter surface

Re: [Freesurfer] Curvature in FreeSurfer

Sent with [ProtonMail](https://protonmail.com) Secure Email. > Original Message > Subject: Re: [Freesurfer] Curvature in FreeSurfer > Local Time: August 16, 2017 4:13 PM > UTC Time: August 16, 2017 2:13 PM > From: fis...@nmr.mgh.harvard.edu > To: Kasper Jess

[Freesurfer] aparcstats2table surface area

Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1.The ROIs extracted are by default the White Surface Area, correct? 2.Why does the WhiteSurfArea (default average) have decimals but not the surface area of the different ROIs? When taking the SUM of all the RO

[Freesurfer] aparcstats2table subject space?

Dear FreeSurfer, When you extract e.g. thickness from the command aparcstats2table - is the data extracted from subject space? We need to know whether or not, we need to covariate for total brain volume. Bw Kasper Kasper Jessen, MD, PhD student Center for Neuropsychiatric Schizophrenia

[Freesurfer] Mean Curvature

Hej FreeSurfer, Question regarding the meancurv extracted from the Desikan atlas using aparcstats2table. Is the meancurv the absolute mean curvature? Thus all the values are positive? Best regards Kasper Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email. Sent with [P

Re: [Freesurfer] Mean Curvature

you for the quick reply. BW Kasper ​Sent from ProtonMail, Swiss-based encrypted email. Sent with ProtonMail Secure Email.​ ‐‐‐ Original Message ‐‐‐ On March 8, 2018 4:13 PM, Bruce Fischl wrote: > Hi Kaspar > > I don't think so. > > cheers > > Bruce

[Freesurfer] Manual editing compared to non-manual editing.

of subjects? Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If