[Freesurfer] Unpacking ASL scans

2018-06-04 Thread Nasiriavanaki, Zahra
Dear Freesurfer developers Hi We collect a new ASL sequence at Bay 4 with Prisma. The scanner outputs a 3D mosaic. The problem is that unpacksdcmdir doesn't seem to work correctly on it so it results to an error! Is there any command other than unpacksdcmdir for unpacking the ASL scans?

[Freesurfer] fcseed-config

2018-07-26 Thread Nasiriavanaki, Zahra
Hi all I am running a seed to whole brain connectivity analysis. I am using the labels that I have made from functional ROIs. When I run fcseed-config, It makes the configuration file but not the .dat files. Here is my command: fcseed-config -segid 1 -seg

Re: [Freesurfer] fcseed-config

2018-07-26 Thread Nasiriavanaki, Zahra
Right! :) Thanks Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf

Re: [Freesurfer] TPEF error

2018-07-18 Thread Nasiriavanaki, Zahra
. Greve Sent: Wednesday, July 18, 2018 2:38:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TPEF error what is your TR? On 07/18/2018 04:03 PM, Nasiriavanaki, Zahra wrote: > > Hi > > > I am running the connectivity analysis (seed to whole brain), and when > I r

Re: [Freesurfer] TPEF error

2018-07-19 Thread Nasiriavanaki, Zahra
04:42 PM, Nasiriavanaki, Zahra wrote: > > 0.8 > > > *Zahra (Mona) Nasiriavanaki* > > Postdoctoral Research Fellow > > Martinos Center for Biomedical Imaging > > Massachusetts General Hospital > > 149 13th Street

[Freesurfer] TPEF error

2018-07-18 Thread Nasiriavanaki, Zahra
Hi I am running the connectivity analysis (seed to whole brain), and when I run selxavg command, I get this error: ERROR: time points in /autofs/space/oprah_001/users/jvm27/looming/all_subjects/liur_loom2_c_sdp/rest/025/TPEF.txt exceed nframes (488) and the time points do not exceed the

Re: [Freesurfer] FsPalm patch

2018-09-07 Thread Nasiriavanaki, Zahra
Hi I downloaded it from this link. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide PALM/UserGuide - FslWiki - University of Oxford fsl.fmrib.ox.ac.uk Downloading and installing PALM. To download latest packaged version, please

Re: [Freesurfer] Errors in scans

2018-06-28 Thread Nasiriavanaki, Zahra
reliable. On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote: > > Hi Freesufer developers > > > We are getting some errors in our resting state and ASL > scans. Everything goes fine while we are scaning the subjects, but > when we look at the data in BORGET, some of them come

[Freesurfer] Errors in scans

2018-06-28 Thread Nasiriavanaki, Zahra
Hi Freesufer developers We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there

[Freesurfer] wm and vcsf nuisance regressors

2019-01-17 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I am using white matter and CSF external nuisance regressors in my mkanalysis-sess. However, when I make these regressors, I use -mean in fcseed-config command, and so the .dat files only have one column (the mean values, I assume). I looked up in the freesurfer archive

Re: [Freesurfer] wm and vcsf nuisance regressors

2019-01-18 Thread Nasiriavanaki, Zahra
or not including those regressors), especially for task-based analysis. On 1/17/19 4:37 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I am using white matter and CSF external nuisance regressors in my mkanalysis-sess. However, when I make these regressors, I use -mean in fcseed-config

[Freesurfer] Freesurfer 5.3 vs 6

2019-01-04 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both recon and preprocessing). My question is whether I can do the first level and group analysis on this data using Freesurfer version 6? Or should I do everything in version 6 from the beginning?

[Freesurfer] gammafit flag in mkanalysis-sess

2019-01-04 Thread Nasiriavanaki, Zahra
Hi Freesurfers I have a few questions about gammafit flag in mkanalysis-sess command and I appreciate if you could respond whenever you had time. -How should we decide which function is best to apply on hemodynamic response signal? I have used both spmhrf and gammafit and I see slightly

Re: [Freesurfer] Freesurfer 5.3 vs 6

2019-01-04 Thread Nasiriavanaki, Zahra
you will never know if the differences you are finding are algorithmic or biological. sorry Bruce On Fri, 4 Jan 2019, Nasiriavanaki, Zahra wrote: > > Dear Freesurfers > > > Hi > > > I have a bunch of data that is preprocessed in Freesurfer version 5.3 (both > recon

Re: [Freesurfer] gammafit flag in mkanalysis-sess

2019-01-04 Thread Nasiriavanaki, Zahra
...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Friday, January 4, 2019 2:26:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] gammafit flag in mkanalysis-sess On 1/4/19 1:27 PM, Nasiriavanaki, Zahra wrote: Hi Freesurfers I have a few questions about

[Freesurfer] exact time of data acquisition per run

2019-03-27 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts Hi I am trying to extract the time of data acquisition for each run from the functional data and compare it with my paradigm files. I thought the numbers in DICOM file names (ie, MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent with the

Re: [Freesurfer] exact time of data acquisition per run

2019-03-27 Thread Nasiriavanaki, Zahra
: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra Sent: Wednesday, March 27, 2019 4:44:14 PM To: Freesurfer support list Subject: [Freesurfer] exact time of data acquisition per run ATTENTION: This email came from an external source. Do not open attachments or click on links

[Freesurfer] projfrac question

2019-02-28 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I was trying to look at the activation in different cortical layers in a single subject. I ran my preproc-sess command three times, once without using -projfrac flag, once -projfrac 0.5 and lastly -projfrac 0.2 The activation patterns are exactly the same. My voxel

Re: [Freesurfer] projfrac question

2019-02-28 Thread Nasiriavanaki, Zahra
thought that it would have changed. Can you look through the logs and find the mri_vol2surf command and verify that the --projfrac argument is changing? On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote: > > Hi Doug > > > Thank you very much for your reply. > > I was actually using -

Re: [Freesurfer] projfrac question

2019-02-28 Thread Nasiriavanaki, Zahra
copy the functional tree to a new location (if you use -p with cp, it will copy the modification time, which will make preproc-sess run faster). On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote: > > Dear Freesurfers > > > Hi > > I was trying to look at the activation in diff

Re: [Freesurfer] projfrac question

2019-03-01 Thread Nasiriavanaki, Zahra
find the commands related to mri_vol2surf? On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote: I did not find mri_vol2surf. Below is part of a log file, as you see -projrfac has changed to 0.5 but not to 0.2. mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg bold/020

[Freesurfer] recon-all -hires

2019-02-21 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts I was running recon-all command with hires flag for our high resolution fMRI data, but it has been in a constant status since yesterday. I copied the last few lines that are currently in my terminal. I had the same issue with another subject before, and I had to

Re: [Freesurfer] projfrac question

2019-03-06 Thread Nasiriavanaki, Zahra
From: Nasiriavanaki, Zahra Sent: Friday, March 1, 2019 11:52:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] projfrac question Yes, I found it. I should mention that, this log file is the result of today's preprocessing (-projfrac 0.2) which I did

Re: [Freesurfer] recon-all -hires

2019-02-22 Thread Nasiriavanaki, Zahra
well. For the subjects where it does complete, do the surfaces look ok? You can also use recon-all.v6.hires with the -conf2hires option (available in fs6 on our network). On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote: Hi Bruce Thank you very much for your reply. Here is my command: recon

Re: [Freesurfer] projfrac question

2019-03-08 Thread Nasiriavanaki, Zahra
e a single project folder (ie, you don't need to copy to a new folder). On 3/7/19 12:20 PM, Nasiriavanaki, Zahra wrote: > > Hi Doug > > > Thank you very much for your reply. > > I ran one of my subjects with the command below and I got this error: > > preproc-sess.test -s $s

Re: [Freesurfer] projfrac question

2019-03-07 Thread Nasiriavanaki, Zahra
. Can you try running that on a subject and see if you get the desired behavior? On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote: > > Hi Doug > > > I re-analyzed one of my subjects from the very beginning with > -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copi

[Freesurfer] tkregister-sess

2019-03-18 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I was checking the functional on structural data registration quality by using the below command. tkregister-sess -s $subj -fsd bold -per-run -bbr-sum I observed high values (around 0.9) for one of my subjects, and I figured out, that subject was registered to another

Re: [Freesurfer] tkregister-sess

2019-03-18 Thread Nasiriavanaki, Zahra
: [Freesurfer] tkregister-sess Did you delete the bad registration file and re-run the registration (preproc-sess)? On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I was checking the functional on structural data registration quality by using the below command. tkregister-sess

Re: [Freesurfer] fcseedcor_multiple runs

2019-02-07 Thread Nasiriavanaki, Zahra
] fcseedcor_multiple runs Looking at the help, it looks like it will produce a separate file for each run for each session. Is that what you want? On 2/1/19 9:41 AM, Nasiriavanaki, Zahra wrote: > > Dear Freesurfers > > > Hi > > > I have been doing seed to seed connectivity

Re: [Freesurfer] fcseedcor_multiple runs

2019-02-15 Thread Nasiriavanaki, Zahra
: Nasiriavanaki, Zahra Sent: Thursday, February 7, 2019 5:39:39 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fcseedcor_multiple runs Thank you so much for your reply. Yes, It does make a separate r and p for each run. But, I would like to have one correlation coefficient for each

Re: [Freesurfer] mri_vol2vol

2019-01-28 Thread Nasiriavanaki, Zahra
on behalf of Greve, Douglas N.,Ph.D. Sent: Monday, January 28, 2019 3:17:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2vol that should work On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually

[Freesurfer] mri_vol2vol

2019-01-28 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I am trying to project a subcortical volume , that I manually made, from fsaverage to individual subject's space. I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my command below: mri_vol2vol --mov ./${ROI}/ROI4.mgz --targ

[Freesurfer] fcseedcor_multiple runs

2019-02-01 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I have been doing seed to seed connectivity analysis using fcseedcor. I have multiple runs for each subject, and based on the fcseedcor help, I am supposed to average runs before comparing across subjects. So, does it mean I should average all seed.dat files and the

[Freesurfer] mri_segstats

2019-04-09 Thread Nasiriavanaki, Zahra
Dear Freesurferers I was trying to do a connectivity analysis using subnuclei of Amygdala. I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked

Re: [Freesurfer] mri_segstats

2019-04-12 Thread Nasiriavanaki, Zahra
From: Nasiriavanaki, Zahra Sent: Thursday, April 11, 2019 4:52:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_segstats Thank you so very much. Yes, the values look normal now. Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of G

Re: [Freesurfer] mri_segstats

2019-04-11 Thread Nasiriavanaki, Zahra
Hi I have not got the answer to my question yet, and I appreciate if you could please let me know what you think about it. Thanks Mona From: Nasiriavanaki, Zahra Sent: Tuesday, April 9, 2019 5:55:58 PM To: Freesurfer support list Subject: mri_segstats Dear

Re: [Freesurfer] mri_segstats

2019-04-11 Thread Nasiriavanaki, Zahra
] mri_segstats You probably need to remove the mean. Add --avgwf-remove-mean to the command line On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote: > > Thank you for your reply. > > The values of mri_segstatsoutput text file (lateral.txt) are high. I > attached it to this email. > &g

Re: [Freesurfer] mri_segstats

2019-04-11 Thread Nasiriavanaki, Zahra
From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, April 11, 2019 4:19:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats The value of what is too high? On 4/11/19 4:07 PM, Nasiriavanaki, Zahra

[Freesurfer] QA_tools citation

2019-05-30 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts Hi I was wondering how should I cite the Freesurfer QA_tools in a paper. I couldn’t find any references in the web page (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools). Thanks Mona ___ Freesurfer mailing list

[Freesurfer] spatial scale bar question

2019-05-10 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain. I couldn't find a scale bar option in Freeview neither. I appreciate if you could

Re: [Freesurfer] spatial scale bar question

2019-05-10 Thread Nasiriavanaki, Zahra
. Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers

Re: [Freesurfer] spatial scale bar question

2019-05-13 Thread Nasiriavanaki, Zahra
/greve/fv.colorbar.gif [https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif] > > > On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote: > > Thanks for your reply. > > I have overlaid the significance map on an inflated brain, and I don't > see the s

Re: [Freesurfer] spatial scale bar question

2019-05-13 Thread Nasiriavanaki, Zahra
Great! Thanks > On May 13, 2019, at 9:56 AM, Bruce Fischl wrote: > > Hi Mona > > sure. As I said it is a bit more complicated than it seems. Ruopeng will post > a note when something usable is in the dev version > > Bruce > > > On Mon, 13 May 2019, Nasi

[Freesurfer] mkanalysis-sess refeventdur

2019-05-20 Thread Nasiriavanaki, Zahra
Hi Freesurfer experts I am making an analysis in Freesurfer version 6 and I have a question about the "refeventdur" in mkanalysis-sess command. My stimulus duration is 16 seconds, but for a specific analysis, I only want to include half of the stimulus duration (ex: the first 8 seconds only

Re: [Freesurfer] mkanalysis-sess refeventdur

2019-05-20 Thread Nasiriavanaki, Zahra
No, you'll need to change your paradigm file to have two distinct 8 sec events rather than one 16 sec event. On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote: > > Hi Freesurfer experts > > > I am making an analysis in Freesurfer version 6 and I have a question > abou

[Freesurfer] funcroi-table-sess

2019-05-07 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts Hi I have a question about funcroi-table-sess, and I appreciate if you could please find a time to reply. Is there anyway that funcroi-sess-table can give out the activation values in each timepoint separately? Right now I can get the average of activation in each

Re: [Freesurfer] mis-registartion question

2019-06-28 Thread Nasiriavanaki, Zahra
y have a small slab of brain in the fMRI. What am I missing? On 6/28/2019 10:41 AM, Nasiriavanaki, Zahra wrote: Thank you so much for your reply. I attached new images. I scrolled through the brain and the worst registration is the last image attached. I'm wondering what else could cause high

[Freesurfer] mis-registration question

2019-08-02 Thread Nasiriavanaki, Zahra
Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject is shown below. Subject 1 10 0.2628 Subject 1 11 0.3038 Subject 1 12 0.7639 Subject 1 13 0.3364 Subject 1 14 0.3346 Subject 1 15

Re: [Freesurfer] spatial scale bar question

2019-08-16 Thread Nasiriavanaki, Zahra
question Hi Mona, If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV. Best, Ruopeng On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra mailto:znasiriavan...@mgh.harvard.edu>>

Re: [Freesurfer] spatial scale bar question

2019-08-16 Thread Nasiriavanaki, Zahra
AM, Nasiriavanaki, Zahra mailto:znasiriavan...@mgh.harvard.edu>> wrote: Hi Ruopeng Thanks for your reply. I have a question though. When I zoom in the 3D image, the scale bar numbers don't change. Shouldn't they change when I zoom in? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Re

Re: [Freesurfer] spatial scale bar question

2019-08-15 Thread Nasiriavanaki, Zahra
tial scale bar question Hi Mona sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version Bruce On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote: > > Yes Bruce. > > It doesn't work. > > I appreciate if you co

Re: [Freesurfer] mis-registration question

2019-08-05 Thread Nasiriavanaki, Zahra
? On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote: Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject is shown below. Subject 1 10 0.2628 Subject 1 11 0.3038 Subject 1 12 0.7639 Subject

Re: [Freesurfer] mis-registration question

2019-08-05 Thread Nasiriavanaki, Zahra
From: Nasiriavanaki, Zahra Sent: Friday, August 2, 2019 12:17:53 PM To: Freesurfer support list Subject: mis-registration question Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject

[Freesurfer] mkcontrast-sess question

2019-09-13 Thread Nasiriavanaki, Zahra
Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single subject functional data with 18 different contrasts, and I am willing to weight the different contrasts as (for example) ascending linear. Something like:

Re: [Freesurfer] Opseq2 question

2019-09-10 Thread Nasiriavanaki, Zahra
to assume a shape to the hemodynamic response, then I don't think it makes much difference. It will make a difference if you are going to use an FIR. On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote: > Hi Freesurfer experts > > I have a question about designing an event related task. We are &g

Re: [Freesurfer] Opseq2 question

2019-09-10 Thread Nasiriavanaki, Zahra
e power. On 9/10/19 11:35 AM, Nasiriavanaki, Zahra wrote: > Hi Doug > > Thank you very much for your reply. How does it make a difference if I > use FIR? Could you please explain a little bit more? > > Thanks > Mona > > *Zahra (Mona) Nasiriavanaki* > > Postdoctor

Re: [Freesurfer] mkcontrast-sess question

2019-09-16 Thread Nasiriavanaki, Zahra
From: Nasiriavanaki, Zahra Sent: Friday, September 13, 2019 11:08 AM To: Freesurfer support list Subject: mkcontrast-sess question Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single subject

[Freesurfer] Opseq2 question

2019-09-09 Thread Nasiriavanaki, Zahra
Hi Freesurfer experts I have a question about designing an event related task. We are designing a task for fear conditioning. Each stimuli presentation lasts 4 seconds. My question is if we set the TR to 2 (which is a multiply of 4), will it make the paradigm to have more power in signal

Re: [Freesurfer] mkcontrast-sess question

2019-09-18 Thread Nasiriavanaki, Zahra
/FsFastParametricModulation On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single subject functional data with 18 different contrasts, and I am willing to weight the different contrasts

Re: [Freesurfer] PALM Analysis

2019-09-19 Thread Nasiriavanaki, Zahra
Hi Doug I wanted to follow up this email and ask you a question. I see in the fspalm page, it says "You can use fspalm with both volume- and surface-based analyses; it will figure everything out". Considering your reply to the below email, I'm wondering if we can use fspalm for subcortical