[Freesurfer] funcroi-table-sess

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] funcroi-table-sess: how to specify frames for multi-band data

Hi Keishi, the frame parameter is the frame in the contrast file. Most of the time this file will only have one frame (-frame 0) unless you have specified a multivariate contrast. This does not have anything to do with multiband. What is your intention when looping through from 0 to 19? doug

[Freesurfer] funcroi-table-sess: how to specify frames for multi-band data

Hi all, I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0 I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used: funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi

Re: [Freesurfer] Funcroi-Table-Sess Error

Thanks!! > On Oct 27, 2015, at 1:18 PM, Douglas Greve wrote: > > > > On 10/27/15 1:09 PM, Morenikeji Adebayo wrote: >> Hi Doug, >> >> Thanks for the help! So, you’re saying that: >> >> By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using >>

Re: [Freesurfer] Funcroi-Table-Sess Error

I think the problem is probably that you created the label from a volume whereas funcroi expects the label to come from a surface. Instead of using mri_cor2label and -label for funcroi-config, try using something like funcroi-config -annot aparc.a2009s G_and_S_cingul-Ant -analysis

Re: [Freesurfer] Funcroi-Table-Sess Error

On 10/27/15 1:09 PM, Morenikeji Adebayo wrote: Hi Doug, Thanks for the help! So, you’re saying that: 1. By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using mri_cor2label, I’ve created volume labels Correct 1. The commands ‘funcroi-config' and 'funcroi-table-sess'

Re: [Freesurfer] Funcroi-Table-Sess Error

Hi Doug, Thanks for the help! So, you’re saying that: By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using mri_cor2label, I’ve created volume labels The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels created on the surface. Is this correct? Thanks,

Re: [Freesurfer] Funcroi-Table-Sess Error

Hi there, Just following up on this. Any help would much appreciated! Thanks, Keji > On Oct 23, 2015, at 1:46 PM, Morenikeji Adebayo > wrote: > > Hi there, > > I ran the following analysis commands: > > mri_cor2label --c >

[Freesurfer] Funcroi-Table-Sess Error

Hi there, I ran the following analysis commands: mri_cor2label --c /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi

Re: [Freesurfer] funcroi-table-sess error, \set: variable name must begin with a letter\

This is a different error: ERROR: cannot find l_ant_cingulate_allVfix.roicfg On 05/19/2015 02:55 PM, Joseph Andreano wrote: Hi Doug, I'm following up on a thread from a few months back, where we were experiencing difficulty with funcroi-table-sess. (You can find the earlier thread here:

Re: [Freesurfer] funcroi-table-sess error, variable must begin with a letter

The log file you sent has a different error: ERROR: cannot find allVfix in NMASA_induction.lh On 02/17/2015 01:40 PM, Joseph Andreano wrote: Hi Doug, We're having difficulty extracting signal from ROIs using funcroi-table-sess. Every time we try, we get the following error message: set:

[Freesurfer] funcroi-table-sess error, \set: Variable name must begin with a letter\

Hi there, I'm having the same problem referenced in this thread from last year. When I send the command: funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 I get

Re: [Freesurfer] funcroi-table-sess error, \set: Variable name must begin with a letter\

I can't remember what the issue was. Can you run funcroi-table-sess -debug -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 | tee dng.log and send me dng.log doug On 12/12/2014 03:03

Re: [Freesurfer] funcroi-table-sess error, set: Variable name must begin with a letter

Hi Katie, can you run it with -debug as the first arg and send me the copious terminal output? doug On 08/30/2013 01:53 PM, Kathryn Devaney wrote: Hi Doug Surfers, I'm having this same issue. I'm running funcroi-table-sess on two analyses (lh and rh). There was no 'log' folder in my

Re: [Freesurfer] funcroi-table-sess error, set: Variable name must begin with a letter

Hi Doug Surfers, I'm having this same issue. I'm running funcroi-table-sess on two analyses (lh and rh). There was no 'log' folder in my working directory, so I created it. Everythingran fine for the lh, but when I try to run it in the rh I get set: Variable name must begin with a letter

[Freesurfer] funcroi-table-sess error, set: Variable name must begin with a letter

Hi All, I'm trying to use funcroi-table-sess, but whenever I send this command: funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305 -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat I get this error: set: Variable name must begin with a letter So far as I can tell, all

Re: [Freesurfer] funcroi-table-sess error, set: Variable name must begin with a letter

Is there a folder called log in the directly you are running it from? If not, try creating one. If so, then run it with -debug as the first arg and send me the terminal output. doug On 08/19/2013 02:07 PM, Joseph Andreano wrote: Hi All, I'm trying to use funcroi-table-sess, but whenever I

Re: [Freesurfer] funcroi-table-sess error

Hi Doug, I was running the command out of the $SUBJECTS_DIR. I created a log folder in the $SUBJECTS_DIR and then the command ran smoothly! Thanks! Best, Alex Hi Alex, are you running it from the project folder? It is looking for a folder called log in the current directory. It should be

Re: [Freesurfer] funcroi-table-sess error

Hi Alex, are you running it from the project folder? It is looking for a folder called log in the current directory. It should be creating this folder (bug). So, if you run it from the project folder, the log folder will be there. Or can create a log folder in your current directory (mkdir

[Freesurfer] funcroi-table-sess error

Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf

[Freesurfer] funcroi-table-sess with multiple contrasts

Hi, Is there anyway to print multiple contrasts in one output file using funcroi-table-sess command? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list

Re: [Freesurfer] funcroi-table-sess with multiple contrasts

sorry, only one contrast doug SHAHIN NASR wrote: Hi, Is there anyway to print multiple contrasts in one output file using funcroi-table-sess command? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D.

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Hi Yuko, The contrast only allows you to constrain the anatomical ROI. If you don't spec a contrast, then it uses the whole anat ROI. Nothing gets averaged until you run funcroi-table-sess, and that only averages over the given contrast (unless you use -vol in which case it just reports the

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Good point! This is a slight bug in the program that it requires a contrast when you ask for the volume. This is because the volume is completely set once you run funcroi-sess, so it won't make a difference what contrast you specify. The contrast only matters when you ask it to report a mean

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Thanks Doug, If I don't specify a contrast with funcroi-config, then, the value I get from funcroi-table-sess is the average across all conditions including fixation? What I want to get is a non-thresholded value for each condition. So I should specify a contrast with funcroi-config, correct?

[Freesurfer] funcroi-table-sess: average baseline activity?

Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Hi Yuko, answers below Yuko Yotsumoto wrote: Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Thanks Doug, On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with funcroi-config? Even easier: just don't specify a contrast.

Re: [Freesurfer] funcroi-table-sess

Doug, Thanks for the reply. Let me clarify two things: 1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with funcroi-config? 2) If I use thresholding, is there a way to output the number of voxels met that criteria with funcroi-table-sess? Best,

Re: [Freesurfer] funcroi-table-sess

Currently, it is not as convenient to do this with version 5. You have to create a condition-vs-fixation for each condition that you want a time course for. Then for each condition, you need to run funcroi-table-sess for each time point (using the -frame option), then construct the waveforms

[Freesurfer] funcroi-table-sess

Hi All, I'm using : freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I'd like to plot HDR for each condition for each subject. With FreeSurfer v4.5.0, I did so with func2roi-sess and roisummary-sess. With v5.0, those commands do not seem to work. I could get a table with: funcroi-config