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

2019-12-21 Thread Tudor Popescu
External Email - Use Caution Dear FS experts, From a pre- 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 aim not so much

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

2018-11-30 Thread Tudor Popescu
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: > > > > > External Emai

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

2018-11-29 Thread Tudor Popescu
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

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

2018-07-04 Thread Tudor Popescu
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

2018-06-21 Thread Tudor Popescu
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

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

2018-06-13 Thread Tudor Popescu
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

2018-06-11 Thread Tudor Popescu
-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 your answer! Befo

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

2018-06-07 Thread Tudor Popescu
o 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. > > cheers > Bruce > > On Wed, 6 Jun 2018, T

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

2018-06-06 Thread Tudor Popescu
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

2018-06-01 Thread Tudor Popescu
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

2014-10-03 Thread Tudor Popescu
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 brain (talairach or MNI) with several

[Freesurfer] Displaying clusters from different QDEC analyses, overlapped

2014-10-02 Thread Tudor Popescu
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.

[Freesurfer] Reporting longitudinal change (pc1)

2014-10-02 Thread Tudor Popescu
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] Masks based on 10-20 locations of stimulating electrodes

2014-09-04 Thread Tudor Popescu
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 F3F4 for one group and on P3P4 in another group (10-20

[Freesurfer] Group differences in pc1 (longitudinal stage2)

2014-07-11 Thread Tudor Popescu
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

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

2014-06-20 Thread Tudor Popescu
? Doesn't variability across all 3 groups somehow have to be accounted for? Tudor On 16 June 2014 20:38, Douglas Greve gr...@nmr.mgh.harvard.edu 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 set with 3 groups (2

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

2014-06-16 Thread Tudor Popescu
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

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

2014-06-16 Thread Tudor Popescu
across all 3 groups somehow have to be accounted for? Tudor On 16 June 2014 20:38, Douglas Greve gr...@nmr.mgh.harvard.edu 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 set with 3 groups (2 treatments, 1 control

[Freesurfer] Computing LGI values for the longitudinal stream

2014-06-10 Thread Tudor Popescu
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

Re: [Freesurfer] Longitudinal design

2014-06-04 Thread Tudor Popescu
everything is generated new). Best, Martin On Jun 2, 2014, at 5:34 PM, Tudor Popescu tud...@gmail.com 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 was wondering whether there's a better way to do

Re: [Freesurfer] Longitudinal design

2014-05-27 Thread Tudor Popescu
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 tud...@gmail.com wrote: Thanks very much Martin and Bruce. I guess I'd misread the Wiki (my own fault, not the text's), and am glad to hear

Re: [Freesurfer] Longitudinal design

2014-05-25 Thread Tudor Popescu
the longitudinal tutorial http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial 3. At the recon all level in FS you get (after the 3 steps) measurement for all time 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

[Freesurfer] surface-based morphometry registration

2014-05-21 Thread Tudor Popescu
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

Re: [Freesurfer] surface-based morphometry registration

2014-05-21 Thread Tudor Popescu
), 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: Hi all, If I understand correctly, the surface-based

Re: [Freesurfer] Longitudinal design

2014-05-08 Thread Tudor Popescu
Sorry for the repeat, wasn't sure whether this was received the first time. Tudor On 6 May 2014 19:55, Tudor Popescu tud...@gmail.com wrote: Dear FS list, I have structural data from a learning study (prepost-training scans, with 3 groups). Although the training was only one week, I'm

[Freesurfer] Longitudinal design

2014-05-06 Thread Tudor Popescu
Dear FS list, I have structural data from a learning study (prepost-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

2014-04-04 Thread Tudor Popescu
on and 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 Tudor On 2 April 2014 12:33, Tudor Popescu tud...@gmail.com

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

2014-04-02 Thread Tudor Popescu
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: Computing

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

2014-03-31 Thread Tudor Popescu
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

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

2014-03-31 Thread Tudor Popescu
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 each of these clusters, to have a list of extracted average thickness

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

2014-03-31 Thread Tudor Popescu
to extract values from the two clusters? On 31 March 2014 18:35, Douglas N Greve gr...@nmr.mgh.harvard.edu 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 Doug

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

2014-03-31 Thread Tudor Popescu
5.3.0 On 31 March 2014 19:07, Douglas N Greve gr...@nmr.mgh.harvard.edu 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 the MC-Z correction) are mc

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

2014-03-31 Thread Tudor Popescu
correction for multiple 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: what version of FS

Re: [Freesurfer] Group comparisons

2014-03-23 Thread Tudor Popescu
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 X age,

Re: [Freesurfer] Group comparisons

2014-03-09 Thread Tudor Popescu
there are significant clusters for that contrast? Many thanks! Tudor On 8 March 2014 10:03, Tudor Popescu tud...@gmail.com 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 probed by the contrast Does the thickness

Re: [Freesurfer] Group comparisons

2014-03-08 Thread Tudor Popescu
Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 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 (randomise) applies the GLM by doing permutations, and so

Re: [Freesurfer] Group comparisons

2014-03-07 Thread Tudor Popescu
16:53, Douglas N Greve gr...@nmr.mgh.harvard.edu 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 (randomise) applies the GLM by doing permutations, and so already corrects for multiple comparisons

[Freesurfer] Group comparisons

2014-03-05 Thread Tudor Popescu
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

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

2014-02-04 Thread Tudor Popescu
/2014 01:55 PM, Tudor Popescu wrote: Dear Freesurfer experts, I ran a QDEC analysis for structural data and found, after Monte-Carlo correction@0.05, one significant cluster, annotated as postcentral (see screenshot attached). The stats associated with it are displayed in the terminal

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

2014-02-04 Thread Tudor Popescu
It does indeed, thanks Doug T On 4 February 2014 18:19, Douglas N Greve gr...@nmr.mgh.harvard.edu 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. I only now gather

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

2014-02-02 Thread Tudor Popescu
the visualisation 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 tud...@gmail.com wrote: Dear Freesurfer experts, I ran a QDEC analysis

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

2014-01-05 Thread Tudor Popescu
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] wm.mgz edits get overwritten surfs not correctly re-generated

2014-01-05 Thread Tudor Popescu
Hi Bruce Yes I am - sorry to not have mentioned Tudor On 5 January 2014 17:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tudor Are you doing the editing with tkmedit? Cheers Bruce On Jan 5, 2014, at 6:20 AM, Tudor Popescu tud...@gmail.com wrote: Hi everyone and happy new year

Re: [Freesurfer] Artefactual skull stripping for some subjects

2013-07-17 Thread Tudor Popescu
. 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 tud...@gmail.com wrote: Hi again, I was wondering whether my previous message was received, since it had rather large attachments

Re: [Freesurfer] Artefactual skull stripping for some subjects

2013-07-15 Thread Tudor Popescu
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 tud...@gmail.com wrote: Thanks Bruce. So the massive chunks

Re: [Freesurfer] Artefactual skull stripping for some subjects

2013-07-09 Thread Tudor Popescu
, 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 artefacts are likely to be the result of the same

Re: [Freesurfer] Artefactual skull stripping for some subjects

2013-07-08 Thread Tudor Popescu
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 tud...@gmail.com wrote: Hi everyone The skull-stripping step of recon-all must have gone bad for my sample, because I noticed

Re: [Freesurfer] Artefactual skull stripping for some subjects

2013-07-08 Thread Tudor Popescu
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 watershed25 and with the -no-wsgcaatlas flag might be the thing

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

2013-06-17 Thread Tudor Popescu
… 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 On Jun 14, 2013, at 11:22 AM, Tudor Popescu tud...@gmail.com wrote: Many thanks for your reply Marie. getmatlab returns ERROR: Cannot

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

2013-06-14 Thread Tudor Popescu
Dear Freesurfer localGI experts, I want to compare local GI (gyrification index) between my two groups. Following the help https://surfer.nmr.mgh.harvard.edu/fswiki/LGI, I ran this command for one of my subjects: recon-all -s M01 -localGI but it resulted in the error:

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

2013-06-14 Thread Tudor Popescu
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. doug On 6/14/13 3:25 AM, Tudor Popescu wrote: Dear Freesurfer localGI experts, I want to compare local GI (gyrification index) between

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

2013-06-13 Thread Tudor Popescu
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] ERROR:: Too many arguments. from recon-all / make_outer_surface

2013-06-13 Thread Tudor Popescu
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 tud...@gmail.com wrote: Hi all, The command: recon-all -s M19 -localGI resulted

[Freesurfer] Group analysis

2013-06-06 Thread Tudor Popescu
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 to

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

2013-06-06 Thread Tudor Popescu
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.white into

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

2013-06-05 Thread Tudor Popescu
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 find a log

Re: [Freesurfer] Bug report: QDEC

2013-05-24 Thread Tudor Popescu
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: after setting a different FDR threshold and pressing

[Freesurfer] Bug report: QDEC

2013-05-23 Thread Tudor Popescu
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

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

2013-05-23 Thread Tudor Popescu
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 have

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

2013-05-22 Thread Tudor Popescu
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

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

2013-05-14 Thread Tudor Popescu
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 tud...@gmail.com wrote: Dear Freesurfer experts, I very much appreciate your help with an additional set

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

2013-05-14 Thread Tudor Popescu
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 and age,..?

[Freesurfer] Still confused by group analysis..

2013-05-12 Thread Tudor Popescu
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

2013-05-11 Thread Tudor Popescu
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

[Freesurfer] Labels and parcellations

2013-05-08 Thread Tudor Popescu
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

Re: [Freesurfer] Labels and parcellations

2013-05-08 Thread Tudor Popescu
pressing some buttons, and some menu options, with no luck) On 8 May 2013 16:54, Douglas N Greve gr...@nmr.mgh.harvard.edu 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 expected

Re: [Freesurfer] Labels and parcellations

2013-05-08 Thread Tudor Popescu
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 mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: On 05/08/2013 11:43 AM, Tudor Popescu

Re: [Freesurfer] ROI analyses

2013-05-02 Thread Tudor Popescu
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 would

[Freesurfer] ROI analyses

2013-04-29 Thread Tudor Popescu
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

Re: [Freesurfer] QDEC questions

2013-04-18 Thread Tudor Popescu
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 tud...@gmail.com wrote: Thanks Nick, (and thanks Doug too for the answer to question 2.) It must indeed have been

Re: [Freesurfer] QDEC questions

2013-04-16 Thread Tudor Popescu
, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote: Dear experts, Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from misbehaving, and so after running a first whole-brain group cortical thickness analysis on my structural data, I have some questions: 1. After running recon-all

Re: [Freesurfer] Error from mri_concat while using QDEC

2013-04-03 Thread Tudor Popescu
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 tud...@gmail.com wrote: Thanks Zeke

Re: [Freesurfer] More QDEC questions

2013-03-29 Thread Tudor Popescu
that the analysis is just an AN(C)OVA, so I still don't understand how questions such as the one about the correlation being non-zero can be answered.. Thanks again very much Doug!! On 28 March 2013 20:07, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 03/28/2013 03:53 PM, Tudor Popescu wrote

Re: [Freesurfer] Error from mri_concat while using QDEC

2013-03-28 Thread Tudor Popescu
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 tud...@gmail.com wrote: Just giving this thread a new bump, as *again *I am receiving this error from mri_concat, upon pressing the Analyze

Re: [Freesurfer] More QDEC questions

2013-03-28 Thread Tudor Popescu
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 tud...@gmail.com wrote: Hi everyone, My QDEC analysis ran into an error

[Freesurfer] More QDEC questions

2013-03-26 Thread Tudor Popescu
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: -

Re: [Freesurfer] Error from mri_concat while using QDEC

2013-03-18 Thread Tudor Popescu
Berger n0642...@students.meduniwien.ac.atwrote: 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 the file name, which should

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

2013-02-25 Thread Tudor Popescu
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

2013-02-04 Thread Tudor Popescu
memory under the 'free' column. confirm that 'recon-all -s bert -all' runs successfully for you prior to running unknown/new data. Nick On Mon, 2013-01-28 at 19:01 +, Tudor Popescu wrote: Hi Nick, Thanks for your help, I'm on Windows XP SP3 VirtualBox 4.2.4

Re: [Freesurfer] Error from mri_concat while using QDEC

2013-02-01 Thread Tudor Popescu
(Virtualbox's shared folder). Anyhow, thanks again for your kind help! Tudor On 31 January 2013 20:36, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 01/31/2013 12:30 PM, Tudor Popescu wrote: Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several

Re: [Freesurfer] Error from mri_concat while using QDEC

2013-01-31 Thread Tudor Popescu
! Tudor On 20 December 2012 05:24, Douglas Greve gr...@nmr.mgh.harvard.edu 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 the full command is mri_concat /media/Dell

Re: [Freesurfer] nu_estimate_np_and_em error during recon-all

2013-01-28 Thread Tudor Popescu
to solve this problem. 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 18 December 2012 17:34, Douglas N

Re: [Freesurfer] nu_estimate_np_and_em error during recon-all

2013-01-28 Thread Tudor Popescu
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!) know where the error that I report earlier in this thread

[Freesurfer] Some beginner questions on cortical thickness analyses

2012-12-18 Thread Tudor Popescu
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

[Freesurfer] Error from mri_concat while using QDEC

2012-12-18 Thread Tudor Popescu
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

[Freesurfer] Contents of SUBJECTS_DIR

2012-12-14 Thread Tudor Popescu
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 *

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

2012-12-06 Thread Tudor Popescu
experienced 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, at 1:47 AM, Tudor Popescu tud...@gmail.com wrote

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

2012-12-05 Thread Tudor Popescu
Hi everyone, I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me repeated Failed to load image name errors. That same image loads fine in FSLview, but even when trying with other NIFTI images, I get the same error. The default image