[Freesurfer] Obtaining pre&post values from longitudinal dataset without cross-base-long

External Email - Use Caution Dear FS experts, From a pre-&post-intervention data set, is it possible to extract thickness values at those two time points just by using recon-all, that is, without running the full longitudinal processing stream (the Cross, Base and Long steps)? I

Re: [Freesurfer] Correspondence between regions of Harvard-Oxford & DKT atlases

r On Thu, 29 Nov 2018 at 16:42, Bruce Fischl wrote: > Hi Tudor > > sorry, I don't think there is a direct correspondence. Is the Oxford > atlas even on the surface? > > cheers > Bruce > On Thu, 29 Nov 2018, Tudor Popescu wrote: > > > > > Ext

[Freesurfer] Correspondence between regions of Harvard-Oxford & DKT atlases

External Email - Use Caution Dear FreeSurfer experts, I have a network of interest described in terms of regions from the Harvard-Oxford atlas. I would next need to describe this network in terms of regions from the DKT (Desikan–Killiany–Tourville) atlas. I have not found hints o

Re: [Freesurfer] Geometries-related error from base step & absent norm.mgz

to be a bug in FS v5.3.0 (which is sadly the only version available to run on Windows, using a Linux Virtual Machine). Cheers, Tudor On Wed, 27 Jun 2018 at 18:00, Tudor Popescu wrote: > Hi again, > > At a loss for more things to try here, I tried the following: for the > first s

[Freesurfer] Geometries-related error from base step & absent norm.mgz

External Email - Use Caution Dear FS list, ( Apologies for asking my question again which I am still struggling to resolve and which I tried to clarify and condense below. ) I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortica

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

more ideas of what I could try, I'd remain really indebted! Cheers, Tudor On Mon, 11 Jun 2018 at 16:03, Bruce Fischl wrote: > Hi Tudor > > I think Martin is probably better able to sort this out than I am. > > Bruce > > > On Mon, 11 Jun 2018, Tudor Popescu wrote: >

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

instead, recon-all -autorecon1 -autorecon2 -subjid 01_1 returns mri_em_register: could not open input volume nu.mgz Not sure what to do at this stage!.. Thanks again for any pointers! Cheers, Tudor On Thu, 7 Jun 2018 at 18:16, Tudor Popescu wrote: > Hi Bruce, > > Thanks for yo

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

ences are trivial you can resample the > images to all have exactly the same geometries and rerun (I think > mri_convert -rl > > should do it (-rl is "reslice like"). If they are not trivial though you > may find effects that only reflect the acquisition differences. > >

Re: [Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

External Email - Use Caution Hello, If any more information is needed to address my question, please do let me know. I hope to hear back and once again thanks a lot for any assistance with this. Best wishes, Tudor On 1 June 2018 at 16:07, Tudor Popescu wrote: > Dear

[Freesurfer] "WARNING: Image geometries differ across time" upon running base step of longitudinal pipeline

External Email - Use Caution Dear all, I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness pre and post, for all standard regions in the atlas, and use those in subsequent analyses. Following the standard approach <

Re: [Freesurfer] Displaying clusters from different QDEC analyses, overlapped

the ribbon > doug > > On 10/02/2014 08:48 AM, Tudor Popescu wrote: > > Dear FS list, > > > > I have significant clusters from several QDEC analyses (each one for a > > different DV< i.e. thickness, area, etc). I would like to generate a > > picture of a standard

[Freesurfer] Reporting longitudinal change (pc1)

Dear FS list (dear Martin), I have a 3 groups x 2 timepoints data set, and I did analyses in QDEC comparing my groups pairwise (2 at a time) in terms of the pre-to-post percentage change (pc1) in various surface-based metrics like thickness and area. Since a group contrast is a bit difficult for

[Freesurfer] Displaying clusters from different QDEC analyses, overlapped

Dear FS list, I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regio

[Freesurfer] Masks based on 10-20 locations of stimulating electrodes

Dear FS team, I have structural data from a training study involving different tDCS groups. I would like to define ROIs (masks) in MNI space corresponding to the approximate cortical area underlying the tDCS electrodes, which were placed on F3&F4 for one group and on P3&P4 in another group (10-20

[Freesurfer] Group differences in pc1 (longitudinal stage2)

Dear FS list, (dear Martin!) I have a longitudinal design, 3 groups, 2 timepoints, and I created three different QDEC tables (two groups at a time) in order to be able to compare each pair of groups in terms of percentage change from pre to post (what's referred to as "pc1" in the first stage of t

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

he fwhm.dat was "10.190419, rounded to 11". I am using FS 5.3.0 (Ubuntu). Thanks! Tudor On 17 June 2014 09:29, Douglas Greve wrote: > > It only needs to be accounted for when you compare across all 3 groups, in > which case you'd have to use mri_glmfit > doug > &

Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points

groups? Doesn't variability across all 3 groups somehow have to be accounted for? Tudor On 16 June 2014 20:38, Douglas Greve wrote: > > Yes, you could do each separately. > doug > > > > On 6/16/14 8:10 PM, Tudor Popescu wrote: > > Dear FS list, > > I have a data s

[Freesurfer] Using QDEC for 3 groups x 2 time-points

Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of the two-stage model, and I would prefer to run stage#2 (cross-sectional analysis of the di

[Freesurfer] Computing LGI values for the longitudinal stream

Dear FS list, I did all 3 steps of the longitudinal stream (cross, base, long), plus the long_mris_slopes for my three-group & two-timepoint data set. This gave me files for thickness and area, but I'd also like to do analysis for lGI. To that end, I first did recon-all -s subj -localGI and the

Re: [Freesurfer] Longitudinal design

scratch (to make > sure everything is generated new). > > Best, Martin > > On Jun 2, 2014, at 5:34 PM, Tudor Popescu wrote: > > Hi Bruce > > I suspected this might be the case, since assessing 3D surfaces from a > succession of 2D slices can be tricky, which is why I

Re: [Freesurfer] Longitudinal design

Hi Martin, Wasn't sure whether you'd seen my reply below, look forward to hear back your thoughts, thanks! Tudor On 25 May 2014 21:40, "Tudor Popescu" wrote: > Thanks very much Martin and Bruce. I guess I'd misread the Wiki (my own > fault, not the text&#

Re: [Freesurfer] Longitudinal design

e points. So you would compare those results across time in the > stats. > > Hope that helps, Martin > > > On 05/08/2014 08:14 AM, Tudor Popescu wrote: > > Sorry for the repeat, wasn't sure whether this was received the first time. > Tudor > > > On 6 May 2014

Re: [Freesurfer] surface-based morphometry registration

e volume), but part is that we register based on > cortical folding patterns not image intensities, so folds are much more > likely to align across subjects (and architectonic areas as well) > > cheers > Bruce > > > > On Wed, 21 May 2014, Tudor Popescu wrote: > &

[Freesurfer] surface-based morphometry registration

Hi all, If I understand correctly, the surface-based morphometry (SBM) done by Freesurfer offers superior registration as compared to voxel-based methods such as VBM, in that: 1. "SBM smoothing respects anatomical boundaries better than the 3D VBM smoothing". 2. "SBM group analysis employs inter-

Re: [Freesurfer] Longitudinal design

Sorry for the repeat, wasn't sure whether this was received the first time. Tudor On 6 May 2014 19:55, Tudor Popescu wrote: > Dear FS list, > > I have structural data from a learning study (pre&post-training scans, > with 3 groups). Although the training was only one we

[Freesurfer] Longitudinal design

Dear FS list, I have structural data from a learning study (pre&post-training scans, with 3 groups). Although the training was only one week, I'm guessing from an analysis point of view, this still qualifies as longitudinal. I want to check for - the main within-subjects effect of time point (

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

d what version of FS? > doug > > > On 04/02/2014 06:34 PM, Tudor Popescu wrote: > >> Hi Doug >> Sorry, again I wasn't sure whether you'd noticed my reply amonst the >> latest list messages. Hopefully there is a fix for this error. >> Thanks >> T

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

> >> Your mri_glmfit-sim command line is not correct and does not match >> examples in the help. Basically you need to spec "--cache 1.3 abs" >> not "--cache 1.3 --sim-sign abs" >> >> Thanks Doug, now it worked, however I'm getting this error, which several >> other people seem to get:

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

ltiple comparisons? > Either from qdec or with mri_glmfit-sim? That y.ocn file should be there > > On 03/31/2014 02:02 PM, Tudor Popescu wrote: > > 5.3.0 > > > > > > On 31 March 2014 19:07, Douglas N Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

5.3.0 On 31 March 2014 19:07, Douglas N Greve wrote: > > what version of FS are you running > > > On 03/31/2014 12:48 PM, Tudor Popescu wrote: > > Hi Doug > > > > The only OCN files I have in my qdec correlation contrast folder > > (after having run

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

extract values from the two clusters? On 31 March 2014 18:35, Douglas N Greve wrote: > > The file you are looking for should be something like > mc-z.abs.th13.y.ocn.dat > you dont need to run mri_glmfit-sim again > > On 03/31/2014 12:25 PM, Tudor Popescu wrote: > > Thanks D

Re: [Freesurfer] extracting mean thickness values across subjects from qdec clusters

gt; more info > doug > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > Dear Freesurfer experts, > > > > After a qdec contrast that asked where does thickness correlate with > > behavioural score, I got 2 significant clusters, and I would like, for > &g

[Freesurfer] extracting mean thickness values across subjects from qdec clusters

Dear Freesurfer experts, After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can

Re: [Freesurfer] Group comparisons

Hi Doug, > 3) In a group X gender X age DODS design, exactly which contrast > > (interaction) has to be examined in order to see if the analysis > > proceeds as DODS or as DOSS? And what would the course of action be > > assuming there are significant clusters for that contrast? > > group X gender

Re: [Freesurfer] Group comparisons

tion be assuming there are significant clusters for that contrast? Many thanks! Tudor On 8 March 2014 10:03, Tudor Popescu wrote: > > Thanks Doug. I wasn't clear in my DOSS question, I meant to ask why >> > are categoricalXcontinuous interactions (e.g. such as the one probe

Re: [Freesurfer] Group comparisons

oticed some contrasts that were wrong, but I was just wondering whether the said contrast ("Does the thickness-age correlation differ between group A and B?") was is in fact ever meant to be computed, as it seems it should not be there by virtue of the definition of DOSS. On 8 March 2014

Re: [Freesurfer] Group comparisons

ependent on the volumetric (T1) resolution? Thanks! Tudor On 6 March 2014 16:53, Douglas N Greve wrote: > > On 03/06/2014 10:35 AM, Tudor Popescu wrote: > > Sorry, couple more questions: > > > > 1) I know that QDEC's/mri_glmfit's equivalent in FSL ("random

Re: [Freesurfer] Group comparisons

h grey matter density? Why even register to the template in the first place if you're then going to go back and use native-space values? Thanks! On 6 March 2014 10:20, Tudor Popescu wrote: > Thank you very much Doug. > Tudor > > > On 6 March 2014 03:53, Douglas Greve

[Freesurfer] Group comparisons

Hello, I have some questions on doing group comparisons with thickness, area and volume. Many thanks in advance for any help! 1) For a DOSS design with group and gender as categorical factors, I see that an interaction contrast ("Is there a group-gender interaction in the mean thickness?") still e

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

It does indeed, thanks Doug T On 4 February 2014 18:19, Douglas N Greve wrote: > > The value displayed is actually sign(effect)*log10(p), which I think > answers both of your questions > doug > > > On 02/04/2014 01:00 PM, Tudor Popescu wrote: > > Thanks Doug.

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

inity. How come, then, that the colour-bar also shows negative values? Tudor On 4 February 2014 17:09, Douglas N Greve wrote: > > You have the "Min" set to 2 which means that you are not seeing cluster > less significant than p=.01. Try setting it to 1.3 (p=.05) > doug > &

Re: [Freesurfer] Significant cluster only shows up in the terminal but not on the template brain

ualisation threshold (you have min = 2), whereas you run your Monte > Carlo with a threshold of 0.05 (i.e. 1.3), and your cluster seem to be just > in between. > > Hope it helps, > > Marie > > > On Feb 2, 2014, at 10:55 AM, Tudor Popescu wrote: > > > Dear Freesurf

Re: [Freesurfer] wm.mgz edits get overwritten & surfs not correctly re-generated

Hi Bruce Yes I am - sorry to not have mentioned Tudor On 5 January 2014 17:00, Bruce Fischl wrote: > Hi Tudor > Are you doing the editing with tkmedit? > Cheers > Bruce > > > On Jan 5, 2014, at 6:20 AM, Tudor Popescu wrote: > > > > Hi everyone and happy new

[Freesurfer] wm.mgz edits get overwritten & surfs not correctly re-generated

Hi everyone and happy new year! I made a couple of manual edits to a wm.mgz file and then relaunched part of that subject's recon (-autorecon2-wm -autorecon3). After it finished, however, the wm.mgz had lost its manual edits - even though I had saved the edited version under the same name, in the

Re: [Freesurfer] Artefactual skull stripping for some subjects

tachments. The questions should be visible in plaintext below, please let me know if I should upload the files on a sharing server Thanks! Tudor On 15 July 2013 19:51, Tudor Popescu wrote: > Hi again, > > I was wondering whether my previous message was received, since it had > rather

Re: [Freesurfer] Artefactual skull stripping for some subjects

Hi again, I was wondering whether my previous message was received, since it had rather large attachments. I look forward to receiving a reply with regards to my questions! Thank you, Tudor On 12 July 2013 16:03, Tudor Popescu wrote: > Thanks Bruce. So the massive chunks that appear

Re: [Freesurfer] Artefactual skull stripping for some subjects

un, then 001 and raw are the same > orig.mgz is the first conformed volume > > doug > > > > On 07/08/2013 12:38 PM, Tudor Popescu wrote: > > Thanks Bruce. I have looked at that part of the wiki but I was > > wondering whether the screenshots at all suggest that all arte

Re: [Freesurfer] Artefactual skull stripping for some subjects

Thanks Bruce. I have looked at that part of the wiki but I was wondering whether the screenshots at all suggest that all artefacts are likely to be the result of the same problem, and that e.g. re-running recon for all subjects with a watershed>25 and with the -no-wsgcaatlas flag might be the thing

Re: [Freesurfer] Artefactual skull stripping for some subjects

Dear FSers, Still haven't got to the bottom of this, any suggestions would be much appreciated, thanks in advance! Tudor On 5 July 2013 17:26, Tudor Popescu wrote: > Hi everyone > > The skull-stripping step of recon-all must have gone bad for my sample, > because I notic

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

that as long as you > can run a recon-all process that way, then the recon-all -lgi will work as > well… but same thing, it will need the getmatlab command to point to the > correct location. > > Hope you will find a way, sorry to be not more helpful, > > Marie > >

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

> On Jun 14, 2013, at 7:20 AM, Douglas Greve > wrote: > > Hi Tudor, the lGI stream definitely uses matlab, so that will be a > problem at some point if not now. I would have thought that it would have > reported that it could not find matalb. Marie would know for sure. >

[Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Dear Freesurfer & localGI experts, I want to compare local GI (gyrification index) between my two groups. Following the help , I ran this command for one of my subjects: recon-all -s M01 -localGI but it resulted in the error: make_outer_surface('/m

Re: [Freesurfer] "ERROR:: Too many arguments." from recon-all / make_outer_surface

PS: Which files/folders will I need to delete after I'll have fixed the problem, before re-running the recon? Or will it just overwrite any left-overs? On 13 June 2013 10:32, Tudor Popescu wrote: > Hi all, > > The command: > > recon-all -s M19 -localGI > > resulted

[Freesurfer] "ERROR:: Too many arguments." from recon-all / make_outer_surface

Hi all, The command: recon-all -s M19 -localGI resulted in: make_outer_surface('/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/media/math/all38subj/M19/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit = ERROR:: Too many arguments. I

Re: [Freesurfer] Still confused by group analysis..

Thanks Doug, > So if I want to use the study-specific "average" subject surface with >> mri_surf2surf, rather than the generic "fsaverage" one, how can this be >> done given that the required ls.white file only exists in the latter but >> not in the former? Can I just rename (or duplicate) ls.wh

[Freesurfer] Group analysis

> > Under fsaverage/surf there is both an lh.white and an lh.white_avg file, >> while under average/surf there's only lh.white_avg. I repeated the >> mri_surf2surf command above with "--s fsaverage" instead of "--s average" >> (since I understand in this case it's the same thing), and then it ran t

Re: [Freesurfer] Still confused by group analysis..

> > C) When running mri_surf2surf, I get an error saying that file >> /surf/lh.white cannot be opened. The 'average' folder produced >> after I ran make_average_subject does not contain a >> /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t >> fin

Re: [Freesurfer] Bug report: QDEC

u should see something > like this: > > > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.2, vwth=4.60487 > Found 0 of 163842 vertices above FDR threshold (of 4.60487) > > > > > On 05/23/2013 03:13 PM, Tudor Popescu wrote: > > Just reporting a GUI bug in QDEC: af

[Freesurfer] Contrast vector & link with folder name and QDEC-generated sentence

Hello, I was wondering whether someone could please explain exactly how values are assigned to each column of the design matrix, when a C.dat contrast vector (e.g. [0, 0, 1, -1]) is created, in the "correlation" as opposed to in the "intercept" types of contrasts ... I am asking this because I ha

[Freesurfer] Bug report: QDEC

Just reporting a GUI bug in QDEC: after setting a different FDR threshold and pressing the "Set Using FDR" button, more often than not the results image doesn’t change accordingly. I noticed that the button only has an effect after moving around the QDEC window and/or waiting a minute or so. Hope

Re: [Freesurfer] Still confused by group analysis..

> > 1) In a design with group and gender as discrete factors and age >> > as a continuous factor, why is it that QDEC only displays the >> > contrast "Does the avg thickness, accounting for gender, differ >> > between group1 and group2?" and not also "..acounting for

Re: [Freesurfer] Still confused by group analysis..

> > > 1) In a design with group and gender as discrete factors and age > > as a continuous factor, why is it that QDEC only displays the > > contrast "Does the avg thickness, accounting for gender, differ > > between group1 and group2?" and not also "..acounting for gender > > a

Re: [Freesurfer] Still confused by group analysis..

Not sure whether anyone'd seen my last email (below). Again apologies for the multitude of questions, I hope this is the last batch for this analysis.. On 12 May 2013 16:45, Tudor Popescu wrote: > Dear Freesurfer experts, > > I very much appreciate your help with an additional se

[Freesurfer] Still confused by group analysis..

Dear Freesurfer experts, I very much appreciate your help with an additional set of questions. I feel I'm really close to getting this finished :) 1) In a design with group and gender as discrete factors and age as a continuous factor, why is it that QDEC only displays the contrast "Does the avg

[Freesurfer] thickness

Hi everyone, I resort to asking some questions here again, after feeling increasingly stupid (maybe just tired) after reading the wiki pages relevant for my analysis (ROI, thickness). 1) How should the contrast vector for a group comparison while factoring out age and gender be built? I didn't qui

Re: [Freesurfer] Labels and parcellations

r the mouse (so a legend to each color, much like in Fig 1 of the Desikan paper) I really appreciate your patience Doug, thanks :) Tudor On 8 May 2013 18:56, Douglas N Greve wrote: > > On 05/08/2013 01:28 PM, Tudor Popescu wrote: > >> >> 2) ..and when would you use a s

Re: [Freesurfer] Labels and parcellations

/jt_rh_pial_freesurfer_tksurfer.png>that I linked to, in which it seems each major structure is identified in its own colour, and these colours fill up the entire brain (there's no grey surface left) > >> On 8 May 2013 16:54, Douglas N Greve > gr...@nmr.mgh.harvard.**edu &

Re: [Freesurfer] Labels and parcellations

pressing some buttons, and some menu options, with no luck) On 8 May 2013 16:54, Douglas N Greve wrote: > > On 05/08/2013 11:43 AM, Tudor Popescu wrote: > > Hello all, > > > > I have some more burning questions, for which I thank you in advance!! > > > > 1) I

[Freesurfer] Labels and parcellations

Hello all, I have some more burning questions, for which I thank you in advance!! 1) I expected that "mri_annotation2label --subject 01 --hemi lh --outdir $SUBJECTS_DIR/myLabels" would give me labels corresponding to structures of the standard FreeSurfer atlas (Destrieux), instead it produced lab

Re: [Freesurfer] ROI analyses

Thanks Doug! If I may follow up: > 3) (I can't see whether there's a tutorial for this, as the main FS > > site seems to be down at the moment) How can a group comparison of CT > > be done inside a given ROI, and in what ways can the ROI be specified? > > I guess the command line version of QDEC

[Freesurfer] ROI analyses

Dear Freesurfers, I am doing an ROI analysis (group comparison) of cortical thickness, and I have some questions that I could use some help with. Many thanks in advance! Tudor 1) I used aparcstats2table to extract CT values for structures from the Destrieux atlas, but I cannot identify some impo

Re: [Freesurfer] QDEC questions

Apologies for my previous long email; if anyone gets a chance to look over the questions I'd be really grateful! Many thanks indeed, Tudor On 16 April 2013 19:40, Tudor Popescu wrote: > Thanks Nick, (and thanks Doug too for the answer to question 2.) > > It must indeed have bee

Re: [Freesurfer] QDEC questions

he 10mm fwhm values > created by qcache are used by the 10mm fwhm selection in qdec). > > Nick > > > > On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote: > > Dear experts, > > > > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from > >

Re: [Freesurfer] Error from mri_concat while using QDEC

Hi Zeke, was wondering if you saw my message. VirtualBox only seems to accept VDI files, so it seems I cannot make use of the new 5.2 version, which is downloadable only as a .TAR.GZ Sorry this is proving so difficult.. T On 1 April 2013 15:29, Tudor Popescu wrote: > Thanks Zeke. I tr

Re: [Freesurfer] Error from mri_concat while using QDEC

on its own, I always get the message > > "Killed" at the command line! > > > > Tudor > > Original Message > Subject: Re: [Fre

Re: [Freesurfer] More QDEC questions

ng non-zero can be answered.. Thanks again very much Doug!! On 28 March 2013 20:07, Douglas N Greve wrote: > > On 03/28/2013 03:53 PM, Tudor Popescu wrote: > > I was wondering if anybody is able to help with (any one of) these > > questions? That would be really helpful

Re: [Freesurfer] More QDEC questions

I was wondering if anybody is able to help with (any one of) these questions? That would be really helpful, as I could not find an answer on the wiki. Many thanks in advance! On 26 March 2013 20:44, Tudor Popescu wrote: > Hi everyone, > > > My QDEC analysis ran into an error messag

Re: [Freesurfer] Error from mri_concat while using QDEC

Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor On 26 March 2013 20:35, Tudor Popescu wrote: > Just giving this thread a new bump, as *again *I am receiving this error > from mri_concat, upon pressing the Analyze but

[Freesurfer] More QDEC questions

Hi everyone, My QDEC analysis ran into an error message that seems to be a "classic" (and, so far, it seems unsolved), from mri_concat, which I've described in a separate message, just sent. I have, however, more theoretical questions about QDEC, which I hope some kind soul will help me with:

[Freesurfer] QDEC issues

Hello everyone, I created a qdec.table.dat for my design (a simple group analysis, with gender as categorical factor and age as continuous factor), and created a gender.levels file containing the values that are found in qdec.table.dat, spellt in exactly the same way (all files attached). However,

Re: [Freesurfer] Error from mri_concat while using QDEC

11:13, Andreas Berger wrote: > On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: > > Hi Doug > > > > Strangely, the basic mri_concat command now worked, and so did the full > > one. I think I initially had a "\" at the end of my command, just after &

Re: [Freesurfer] \"nu_estimate_np_and_em\" error during recon-all

Thanks Nick and Anil! I tried with the Bert data set in its original location, and got a different kind of error: ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

_HOME/mni , as they should Still cannot get recon-all to run because of the error mentioned previously & currently at my wit's end! :( On 4 February 2013 10:29, Tudor Popescu wrote: > Hi NIck, > > I too thought disk space might be an issue, however I''ve been runni

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

t;> comes with the distribution, and nuintensitycor is the stage that > >> runs > >> >> nu_correct. > >> >> > >> >> I noticed in your recon-all.log file this line: > >> >> > >> >> total used

Re: [Freesurfer] Error from mri_concat while using QDEC

located on the same partition (Virtualbox's shared folder). Anyhow, thanks again for your kind help! Tudor On 31 January 2013 20:36, Douglas N Greve wrote: > > On 01/31/2013 12:30 PM, Tudor Popescu wrote: > >> Hi Doug, >> >> I'm not sure why that does no

Re: [Freesurfer] Error from mri_concat while using QDEC

your help! Tudor On 20 December 2012 05:24, Douglas Greve wrote: > > That does not make sense. Try using only one input file. Also, put --debug > as the first option. > doug > > > > > > > On 12/19/12 8:32 AM, Tudor Popescu wrote: > > Hi Doug, > So

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

VirtualBox version you are > running this on? I'm at a loss as to why this build no longer works. > > Nick > > > On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote: > > Dear Nick, > > > > I was wondering whether you (or indeed anyone else reading this!)

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

m. Maybe Nick knows. > doug > > > On 12/19/12 6:59 AM, Tudor Popescu wrote: > > Hi Doug, thanks for replying, here is the file attached. In case the > attachment doesn't go through please let me know if I should send it to a > different address. > Tudor > > On

[Freesurfer] "nu_estimate_np_and_em" error during recon-all

Hello, First of all, apologies for asking for help three times today! THings will hopefully become clearer once I get used to FS a bit; I really do appreciate the amazing support provided by the team behind FreeSurfer! I ran the following command on one of my structurals: *recon-all -subject M01

[Freesurfer] Error from mri_concat while using QDEC

Hello everyone, I tried doing the QDEC group analysis tutorial, however after doing everything as instructed in the tutorial, when pressing Analyze I get the error message: *Error in Analyze: command failed: mri_concat /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.m

[Freesurfer] Some beginner questions on cortical thickness analyses

Dear all, I have some questions I could not find an answer to myself, I'd really appreciate it if anyone could help out. 1) How should recon-all be used to process all subjects' data (i.e. obtain the surface for each subject) before taking it to QDEC (or command prompt) for a group thickness anal

[Freesurfer] Contents of SUBJECTS_DIR

Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in * /media/Dell/_FS/buckner_data/* (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of * /home/virtualu

Re: [Freesurfer] Error upon trying to load NIFTI image in freeview

xperienced with Freeview, but did you try typing "freeview" > in the command line and using the File->Load Volume… from the GUI? > If that doesn't work maybe you can give me the exact command you used. > > Hope I could help. > Regards, > Yaniv > On 06/12/2012,

[Freesurfer] Error upon trying to load NIFTI image in freeview

Hi everyone, I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me repeated "Failed to load " errors. That same image loads fine in FSLview, but even when trying with other NIFTI images, I get the same error. The default image (/home/virtualuser/freesurfer/subjects/bert/mri/brainm