Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Re: [Freesurfer] 4 questions regarding Optseq (FS mailing list)
by Douglas N Greve 07 Dec '16

07 Dec '16

Hi Xavier, please remember to post to the FS list. Answers below On 12/07/2016 08:19 AM, Xavier Guell Paradis wrote: > Dear Dr. Greve, > Thank you very much for your reply. I have one last question, which I > think is a very basic concept that I understood wrong: > If I want to compare finger tapping (for periods of 8s) vs. rest (for > periods of 8s), shouldn't I enter "fingertapping" and "rest" as two > conditions (i.e. two events, "ev") in Optseq? No, you do not. > If I do this, then Optseq will generate inter-stimulus intervals, and > my schedule will look more or less like this: > > Fingertapping 8s > NULL 1s > Rest 8s > NULL 4s > Rest 8s > NULL 2s > Fingertapping 8s > etc... > > My question #3 made reference to this: does it make sense that "NULL" > (the interstimulus interval) and "Rest" are essentially the same thing > (the subject is viewing a fixation cross and not doing finger > tapping)? Or should I use only one condition (Fingertapping) (i.e. > only one "event", "ev"), and compare BOLD signal in the fingertapping > condition with BOLD signal in the NULL condition? I would use one condition. > I think the basic question that I am not understanding correctly is > this: If one of the conditions that we want to compare is simply > viewing a fixation cross, should we include this as a condition in > Optseq (i.e. as an event, "ev"; which is the "Rest" in the example > schedule above) or should we just use the inter-stimulus interval > (NULL) as our "viewing a fixation cross" condition? I would not include Rest as a condition in optseq > > Thank you very much, > Xavier Guell. > > Xavier Guell Paradis, M.D. > Visiting Scientist > Massachusetts Institute of Technology > McGovern Institute for Brain Research > Office: 46-4033A > Phone: (617) 324-4355 > Email: xaviergp(a)mit.edu > > On 12/06/2016 04:57 PM, Xavier Guell Paradis wrote: > > > > Dear FS team, > > > > We are designing an fMRI experiment that has to include one motor, one > > cognitive and one affective task. We would like to use a rapid > > event-related design because we want to do MVPA to classify patients > > vs controls. We have 4 questions regarding Optseq: > > > > 1) We are designing a task where subjects either rest (while viewing a > > fixation cross) or tap their right index finger (while viewing a > > fixation cross surrounded by a green circle). Does it make sense, for > > a rapid-event related design, to make subjects tap their right index > > finger for 8 seconds or rest for 8 seconds, or should we decrease the > > number of seconds? > > > From an analysis standpoint, that is fine. optseq will set the number > of seconds for the rest period (you can set the bounds with --tnullmin > and --tnullmax) > > > > 2) We have a similar question for a task where subjects view images > > which are either happy, scary or neutral. Each image lasts 1.5s. We > > would like to group images in groups of 4 so that the emotional > > response is more intense (if we are interested in making the subject > > feel happiness we would prefer that subjects see 4 consecutive happy > > images, rather than one happy image and then one scary image and then > > one happy image). Therefore, we have groups of 4 images and each group > > lasts 6s (4x1.5s). Does it make sense, for a rapid-event related > > design, to consider that each stimulus lasts 6 seconds (this includes > > 4 images of 1.5s of the same emotional category); or should we > > decrease the number of seconds; or simply present each image of 1.5s > > individually? > > > Again, ok. > > > > 3) We are designing a task where subjects either rest (while viewing a > > fixation cross) or tap their right index finger (while viewing a > > fixation cross surrounded by a green circle). Optseq generates > > jittered inter-stimulus intervals, and during inter-stimulus intervals > > subjects will view a fixation cross and rest. Does it make sense that > > subjects are seeing the same thing in the ?rest? condition and in the > > inter-stimulus intervals? (in both cases, a fixation cross is shown in > > the screen and subjects are resting) > > > Isn't this the same as #1? I guess I don't understand how you plan to > analyze your data. Is some of the rest different than other parts of the > rest? > > > > 4) We are designing a go/nogo task where subjects have to press a > > button only when a stimulus of a particular shape (square or circle) > > and color (yellow or purple) is presented. Each stimulus is presented > > for 2s. We would like to change the instructions every 12 stimuli, and > > we would like to change the instructions 3 times. To change the > > instructions, we would have to show text to the subjects for 15 > > seconds explaining the new instructions (e.g. ?press the button when > > you see a purple square?). Is there any way to include the > > instructions in Optseq; or should we run Optseq for 12 stimuli, keep > > the best 4 schedules, and then include a 30 seconds pause between each > > schedule of 12 stimuli to allow the hemodynamic response to return to > > baseline while presenting the new instructions? > > > There is not a way to include the instructions in optseq. I would keep > the best 12-stimulus sequences from optseq. You don't need to wait 30 > sec, 15 sec should be ok > > > > Thank you very much, > > > > Xavier Guell. > > > > > > > > Xavier Guell Paradis, M.D. > > Visiting Scientist > > Massachusetts Institute of Technology > > McGovern Institute for Brain Research > > Office: 46-4033A > > Phone: (617) 324-4355 > > Email: xaviergp(a)mit.edu > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
by Hao wen 07 Dec '16

07 Dec '16

Hello, FS experts: I have a question for visualizing statistical analysis asegstats2tbale result into a map like what we have done in qdec, which uses the thickness information, so if i want to use the volume information of the different segmentation volume, and after doing z-score for two groups, how can I visualize it into a z map??? For example, for the volumetric group analysis, I compute the z-scores for the different subcortical volumes between these two group, how do i visualize the result in sphere??? Really need your help Any help will be appreciated Hao

3 6

'Did not find any volume geometry information in the surface'
by Shady Rahayel 06 Dec '16

06 Dec '16

Hi, I was conducting GLM analysis using the command line. Everything seemed to work fine until I wanted to visualize the uncorrected significance map using the following command (my glmdir folder for the contrast is lh.scheme1.glmdir): freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=$SUBJECTS_DIR/qdec/lh.scheme1.glmdir/scheme1/sig.mgh:overlay_threshold=4,5 -viewport 3d 'Did not find any volume geometry information in the surface' appears in the terminal window. In freeview, only the fsaverage lh.inflated file appears. I am wondering whether it is actually related to my experimental scheme. I want to study the relationship between cortical volume and variable X, while isolating for the effects of 4 factors (2 discrete A and B, 2 continuous C and D). So I've created an FSGD file: GroupDescriptorFile 1 Title xxx Class A1B1 Class A1B2 Class A2B1 Class A2B2 Variables X C D Input .... And I have created a scheme1.mtx contrast matrix that goes like this: 0 0 0 0 0.25 0.25 0.25 0.25 0 0 0 0 0 0 0 0 So that only the slope for X is modelled while isolating for the effect of everything else. I am however unsure of whether it is the proper way to conceptualize the issue. I've done mris_preproc --fsgd scheme1.fsgd --cache-in volume.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.scheme1.volume.15.mgh And then mri_glmfit --y lh.scheme1.volume.15.mgh --fsgd scheme1.fsgd dods --C scheme1.mtx --surf fsaverage lh --cortex --glmdir lh.scheme1.glmdir I am clueless of where may be my mistake. Thank you Shady -- *Shady Rahayel* Étudiant au Ph.D. en neuropsychologie R/I Université du Québec à Montréal Centre d'Études Avancées en Médecine du Sommeil Hôpital du Sacré-Coeur de Montréal

2 1

4 questions regarding Optseq
by Xavier Guell Paradis 06 Dec '16

06 Dec '16

Dear FS team, We are designing an fMRI experiment that has to include one motor, one cognitive and one affective task. We would like to use a rapid event-related design because we want to do MVPA to classify patients vs controls. We have 4 questions regarding Optseq: 1) We are designing a task where subjects either rest (while viewing a fixation cross) or tap their right index finger (while viewing a fixation cross surrounded by a green circle). Does it make sense, for a rapid-event related design, to make subjects tap their right index finger for 8 seconds or rest for 8 seconds, or should we decrease the number of seconds? 2) We have a similar question for a task where subjects view images which are either happy, scary or neutral. Each image lasts 1.5s. We would like to group images in groups of 4 so that the emotional response is more intense (if we are interested in making the subject feel happiness we would prefer that subjects see 4 consecutive happy images, rather than one happy image and then one scary image and then one happy image). Therefore, we have groups of 4 images and each group lasts 6s (4x1.5s). Does it make sense, for a rapid-event related design, to consider that each stimulus lasts 6 seconds (this includes 4 images of 1.5s of the same emotional category); or should we decrease the number of seconds; or simply present each image of 1.5s individually? 3) We are designing a task where subjects either rest (while viewing a fixation cross) or tap their right index finger (while viewing a fixation cross surrounded by a green circle). Optseq generates jittered inter-stimulus intervals, and during inter-stimulus intervals subjects will view a fixation cross and rest. Does it make sense that subjects are seeing the same thing in the “rest” condition and in the inter-stimulus intervals? (in both cases, a fixation cross is shown in the screen and subjects are resting) 4) We are designing a go/nogo task where subjects have to press a button only when a stimulus of a particular shape (square or circle) and color (yellow or purple) is presented. Each stimulus is presented for 2s. We would like to change the instructions every 12 stimuli, and we would like to change the instructions 3 times. To change the instructions, we would have to show text to the subjects for 15 seconds explaining the new instructions (e.g. “press the button when you see a purple square”). Is there any way to include the instructions in Optseq; or should we run Optseq for 12 stimuli, keep the best 4 schedules, and then include a 30 seconds pause between each schedule of 12 stimuli to allow the hemodynamic response to return to baseline while presenting the new instructions? Thank you very much, Xavier Guell. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xaviergp(a)mit.edu

2 1

Problem with mri_vol2surf
by Ilaria Mazzonetto 06 Dec '16

06 Dec '16

Hi Freesurfer User, I would like to map a volume to a surface. I have a T1 image (SubjX) with resolution 1x1x1 and a gray matter mask with resolution 6x6x6. The voxels in the lower resolution image (gm_values.nii) have zero value if they are not in the gray matter and a value between 0.1 and 20 if they are in the gray matter. What I want to do is mapping this values in the pial surface. I runned recon-all with T1 image and I coregistered the lower resolution image (the mask) to higher resolution image with FSL (gm_values2anat.nii). Then I runned mri_vol2surf -- src gm_values2anat.nii --regheader SubjX --hemi lh --surf pial --o gm_values_lhsurf.mgh. I do not understand what the options for surface normal projection mean. I inspected the result with tksurfer, setting fminmask 0 20, and there are a lot of holes. Do you think there is something wrong in what I did? Any help would be greatly appreciated. Regards. Ilaria

2 1

aparcstat2label command result does not include corpuscallosum label
by Hao wen 06 Dec '16

06 Dec '16

Hello, freesurfer experts: I have a question, recently, I use the aparcstats2label comamnd, and get the result file, and I use tksurfer to display the desikan atlas(?h.aparc.annot), and I want to corresponds the labels between this two, but in my aparcstats2label result file, i can not find the corpuscallosum which is the No.4 label in tksurfer, to be specific, here is the label ID in desikan atlas in tksurfer: aparc_lables = ['unknown', 'bankssts', 'caudalanteriorcingulate', 'caudalmiddlefrontal', 'corpuscallosum', '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', 'superiortemporal', 'supramarginal', 'frontalpole', 'temporalpole', 'transversetemporal', 'insula'] which has 36 labels, and I dont understand which label is unknow.... on the contrary, the result from aparcstat2table have 36 columns(includint subject_id and meanthickness), so bacially, they have just 34 labels add one 'unknown', it should have 35 labels, but I did not find the lable 'corpuscallosum', Can someone help me??? The result file for aparcstat2table file is attached:) Thanks in advance

3 5

Cortical thickness and FS-FAST on cerebellum
by stdp82＠virgilio.it 05 Dec '16

05 Dec '16

Hi list,I wonder whether is possible to:1) obtain cortical thickness from cerebellum and its subregions2) use cerebellum (or its subregions) as seed for FS-FAST analysis? Thanks in advance Kind regards Stefano

3 2

Re: [Freesurfer] bbregister --init-reg not working (reg2subject --r returning empty string)
by Antonin Skoch 05 Dec '16

05 Dec '16

Dear Doug, yes, the point is, that my_initial_lta.lta does not have subject name in it. Your suggestion to rearrange parameters in bbregister indeed helped to get further, however, later ended with error in bbregister execution in call of mri_segreg, which does not pass the subject parameter and reads it from the .reg file: mri_segreg --mov /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/template.nii --init-reg /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/init.reg.5112.dat --out-reg /hydradb/hydra_io/vypocty/skoch/20160609_HCENAT_DWI/proc/HCE_C00573_20160524_1456_2/reg/tmp.bbregister.5112/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 The error is: mghRead(/hydradb/hydra_io/vypocty/skoch/20161008_HCENAT_struct/A_HCP_w_FS_dev_long/subject-unknown/mri/orig.mgz, -1): could not open file I solved the issue by additional appending subject id into my_initial_lta.lta file. It seems to work OK, bbregister finishes without error. Antonin ---------------------------------------------------------------------------------------------------- does my_initial_lta.lta have the subject name in it? If not, then put that argument before the --s On 12/05/2016 10:34 AM, Antonin Skoch wrote: > Dear experts, > > I am having trouble using --init-reg option in bbregister (FreeSurfer > v6 beta version). It exits with error: must supply subject id. > > My command line is: > bbregister --mov my_moveable.nii.gz --s my_subject_id --lta > my_lta_out.lta --dti --init-reg my_initial_lta.lta > > I traced the problem to reg2subject --r my_initial_lta.lta which is > executed inside bbregister. This script returns empty string. By > examining reg2subject code, it in case of .lta searches for string > "subject" in lta file. However there is no such string in my .lta. > > My .lta file was created by tkregister2 by conversion from fsl .mat > file (without specification of subject) by command: > > tkregister2 --mov mov.nii.gz --targ targ.nii.gz --ltaout mov2targ.lta > --fsl mov2targ.mat --reg /tmp/junk --noedit > > where mov2targ.mat is vox2vox fsl-style matrix encoding transformation > from mov.nii.gz to targ.nii.gz. I checked validity of produced .lta > file by tkregister2 and it looks OK. > > The straightforward remedy in my case possibly would be to remove > reg2subject invocation from bbregister (since I am already providing > the subject by --s option), or add subject id to .lta. > > General solution in bbregister code would possibly be to provide test > whether subject id is specified and in case it is not, then read the > subject id from registration file. Or read both and in case of > non-empty return of reg2subject, then compare obtained subject id with > subject id supplied by --s and in case of different strings, produce > a warning and use one of them (--s would take precedence?). > > My second inquiry is following: My idea was to do the registration in > 3 stages: provide rough alignment with .lta, then mri_coreg (or > fsl-flirt) and then bb-registration. My experience is, that in some > situations when the images are very differently aligned, the > --init-fsl totally fails. > > Is it possible to realize it by supplying both --init-reg and > --init-coreg (or even combination of --init-reg --init-best to try > both mri_coreg and flirt)? > > Regards, > > Antonin Skoch

1 0

Odd Extremely High/Low Banding of Functional Values in Volume
by Dowling, Kevin Francis 05 Dec '16

05 Dec '16

Hello Freesurfer Experts, I’m attempting to look at activity in a working memory paradigm using blood folate levels as my covariate of interest while controlling for gender and age in 137 subjects. There were no errors (that I could find) in the concatenation or mri_glmfit commands, and subject registration looked ok for the functional data. When visualizing the right and left hemisphere surface sig.mgh files using tksurfer everything looks reasonable. However, when using tkmedit (tkmedit fsaverage1 orig.mgz –overlay sig.mgh –fminmax 1.3 3.3 –fmid 2.3) I am getting odd continuous bands of incredibly high and incredibly low activation spanning throughout most the volume (I’ve attached some screen grabs – the functional values in these bands are either 10000000000 or -10000000000 and look continuous from slice to slice). I’ve taken a look at the list and was not able to find a similar problem discussed. I would be most grateful for any guidance or trouble shooting suggestions you might have! I’ve also attached a text file copy of the glm and tkmedit results in case they would be of use. I'm using Freesurfer version 5.3 (nmr-stable53-env) on a Linux (Release 6.7 (Santiago), Kernel Linux 2.6.32-573.12.1.el6.x86_64 and GNOME 2.28.2) Thank you! Kevin Kevin Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) (617) 643 - 2479

2 1

Edit to wm.seg.mgz.
by miracooloz＠gmail.com 05 Dec '16

05 Dec '16

3 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2016