[Freesurfer] Possible to constrain FDR to a label in the volume?
Dear FreeSurfers, I've created a basal ganglia label and am wondering if it's possible to constrain the FDR calculation to that label? Based on earlier messages it seems like tksurfer has a "marked label only" option for FDR, but I haven't been able to find something similar in tkmedit. Any help greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Possible to constrain FDR to a label in the volume?
Hi Doug. Yup, the FDR button is working for me in tkmedit. I see the mask to brain, but as you can probably guess I'm interested in masking to the basal ganglia. DD From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tuesday, December 02, 2008 12:04 PM To: Dan Dillon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Possible to constrain FDR to a label in the volume? Yea, there's not a mask to label. There is a mask to brain, but I'm not sure if you can substitute your own mask for it. I just tried to run it, and could not get FDR to work at all in tkmedit. Is it working for you at all? doug Dan Dillon wrote: Dear FreeSurfers, I've created a basal ganglia label and am wondering if it's possible to constrain the FDR calculation to that label? Based on earlier messages it seems like tksurfer has a "marked label only" option for FDR, but I haven't been able to find something similar in tkmedit. Any help greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Command works in optseq, not optseq2
Dear FreeSurfers, I'm having a little trouble getting something that works in optseq to work in optseq2. Here's what' is going on . . . when I run this command, things work fine and I get 6 nice sequences: optseq -ntp 170 -TR 3 -npercond 4 4 4 4 4 4 -tpercond 17 17 17 17 17 17 -label NgReal NgLook NgPhoto NuReal NuLook NuPhoto -nsessions 6 -nruns 1 -timewindow 20 -prestim 4 -nsearch 50 -o OptseqTEST However, when I run this command (i.e., my best translation of the previous command into optseq2), I get an error saying that all my schedules are ill-conditioned and I need more scan time or fewer repetitions: optseq2 --ntp 170 --tr 3 --psdwin 0 20 1 --ev NgReal 17 4 --ev NgLook 17 4 --ev NgPhoto 17 4 --ev NuReal 17 4 --ev NuLook 17 4 --ev NuPhoto 17 4 --nsearch 100 --nkeep 6 --o Optseq2TEST Is this a substantive difference between optseq and optseq2 or did I make a mistake with my optseq2 command? Also, I'm assuming there is a reason why I should use optseq2 rather than optseq, but I don't know what it is. Can someone clue me in? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dil...@wjh.harvard.edu> dil...@wjh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Incorporating T2 and T1 images in recon-all
Dear FreeSurfers, I have 2 identical structural scans for my subjects: one is T1-weighted and the other is T2-weighted. Is it possible to pass both scans to recon-all? The T1-scans are rapidly acquired MEMPRAGEs, and recon-all seems to be having some difficulty distinguishing cortex from dura around the sagittal sinus. I thought adding the T2-weighted scan into the mix might improve things a bit. Can this be done, and if so, how? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dil...@wjh.harvard.edu> dil...@wjh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Slice Time Correction Error
Hi all,
We are trying to implement a slice-time correction ('stc-sess -i fmc -o
fmcstc -so siemens -s FPPREW01 -d .') but we get the following error...
INFO: set hdr.hist.orient to -1 /net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional
slicetimer -i
/net/tucson/Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/FPPREW01/bold/013/tmp.10997/in.img
-o /net/tucson/Raid/shart slicetimer:
/usr/lib/libstdc++.so.5: version `GLIBCPP_3.2.2' not found (required by slicetimer)
Is there a simple way to address this issue? Thanks, Dan Dillon
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem with T1 intensities
Dear FreeSurfers, I have a subject whose T1.mgz white matter values are consistently around 160, instead of 110. I figure I will have to tweak mri_normalize and re-run autorecon1 to fix this--am I right? If so, any tips regarding what flags and arguments will help address this problem? Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Register.dat for mri_volcluster
FreeSurfers, I am using mri_volcluster on the output of a fixed-effects analysis, but am getting an error regarding my register.dat file. The register.dat file I'm directing mri_volcluster to is in the group's tal-ffx directory and lists subject "talairach". mri_volcluster is thus looking for subject "talairach" in my SUBJECTS_DIR. The problem is there's no such subject in SUBJECTS_DIR. Here's the message-ERROR: cannot find subject talairach in /exp/REfMRI/mg_2_21/structurals/. How do I fix this? Is a Talairach subject supposed to be put in SUBJECTS_DIR when I run func2tal-sess, or is this a part of a library I should have somewhere? Or do I create this file? Any help would be appreciated. Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about trials w/subject errors
Dear FreeSurfers, We are running a paradigm that occasionally elicits erroneous responses from subjects. In our mkanalysis step, we have 13 conditions-10 are legit, and codes 11, 12, 13 correspond to various kinds of errors. Thus, we only use the first 10 codes in mkcontrast, etc. However, occasionally we have a subject who makes no errors. How should we account for this? Is it okay to just change the # of conditions in the mkanalysis .info file (from 13 to 10) and then run selxavg on these folks? Can we then average their data in with people who have all 13 conditions? Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Output of mri_volcluster
Dear FreeSurfers, I'm trying to replicate some functional analyses that were originally done in SPM2, and am using mri_volcluster. Here's my command: mri_volcluster --in Old8/bold/taumax30_2_21/tal-ffx/RSF_v_NIF/sig --in_type bfloat --reg Old8/bold/taumax30_2_21/tal-ffx/register.dat --thmin 3 --minsizevox 8. I've noticed that the size (in voxels) and number of clusters changes if I play with the -sign flag. I am confused by this. Here's the output not using the -sign flag: Cluster Size(n) Size(mm^3) TalX TalYTalZ Max 1 28 1792.0 -19.80 -96.708.53 5.28907 2 8512.0 39.60 26.79 -8.07 4.15380 3 9576.0 99.00 16.69 -54.67 4.09661 4 10640.0 87.12 63.11 18.95 -3.82155 5 13832.0 67.32 -42.445.81 3.79067 6 11704.0 -39.60 -16.43 59.78 -3.62503 7 11704.0 -87.12 -75.98 -43.30 -3.59305 8 73 4672.0 43.56 -22.33 19.54 -3.43893 9 18 1152.0 43.56 -44.81 -41.49 -3.16065 10 8512.0 -51.48 -32.30 53.20 -3.09981 11 15960.0 -63.36 -20.49 56.30 -3.00613 12 48 3072.0 -71.28 -7.20 11.41 -3.00547 And here's the output with sign set to positive: Cluster Size(n) Size(mm^3) TalX TalYTalZ Max 1 35 2240.0 -19.80 -96.708.53 5.28907 2 21 1344.0 39.60 26.79 -8.07 4.15380 3 13832.0 99.00 16.69 -54.67 4.09661 4 10640.0 -71.28 33.20 -35.31 3.91335 5 21 1344.0 67.32 -42.445.81 3.79067 6 9576.0 35.64 -88.58 15.49 3.63267 Why does the size of the first cluster change? Also, where is cluster 4 from the second output in the first output? Is there some re-calculation going on here? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Temporal derivative in mkanalysis-sess
Dear FreeSurfers, I'd like to add a temporal derivative to my gammafit model and understand that this can be done using mkanalysis-sess. However, I can't seem to track down the relevant flag (using -help or the wiki). Can someone point me in the right direction? Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Where to get mri_binarize?
I would like to use mri_binarize but don't seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Gammafit vs. SPMHRF
Dear FreeSurfers, What exactly is the difference between the HRF function in gammafit vs. SPMHRF? Are there reasons to prefer one to the other? Thanks, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Masking group data using mri_volcluster
Dear FreeSurfers, I've run some fixed and random effects analyses in Talairach space and would like to constrain the output of mri_volcluster to areas within the brain (e.g., not the eyeballs). How do I create a brainmask that is the same dimensions as the input volume I pass to mri_volcluster? Without a mask, I'm currently getting stats on extra-brain voxels that I do not want, and I can't use the Talairach brainmask.mgz file b/c it doesn't match my input volume. Any help would be appreciated. Dan Dillon PS. The command I'm currently running, sans mask, is as follows: mri_volcluster --in LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/Rcue_v_Ncue/sig --in_type bfloat --reg LowTrauma/bold/LowTraumaSPMHRF/tal-ffx/register.dat --thmin 3 --minsizevox 12 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Masking at the individual level
Dear FreeSurfers,
Quick question about masking. I routinely make a brainmask for each subject
and include the mask flag in the mkanalysis (see below), but I note that
when I run contrasts and plot results-either for individual subjects or for
group-level stuff-I get statistical results for voxels outside the brain.
I'd like to mask the extra-brain voxels out at the individual level, so that
they don't get included at any point in my group level analyses. How do I do
this? More generally, does the brainmask serve only a visual/display
function or can I use it to constrain what I'm doing stats on (which is what
I want it to do)?
Thanks for your endless help!
Dan Dillon
PS. This is a a typical mkanalysis step . . .
mkanalysis-sess.new -analysis ${analysis} -gammafit 2.25 1.25 -TR 2.5
-paradigm mg_3_7.par -designtype event-related -funcstem fmcs
tcsm6 -nconditions 13 -polyfit 2 -taumax 30 -inorm -mask brain -timeoffset
-1.25 -TER .1 -autostimdur -force
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] How to extract beta weights, by condition, for whole-brain regression analysis
Dear FreeSurfers, I have completed individual and group level functional analyses using FS-FAST, and would like to correlate individual differences in self-report measures against the betas for several of my 13 conditions (I used -gammafit in mkanalysis). My questions are: 1) Where are the beta weights located? and 2) How do I extract beta weights for each condition for each participant? I suspect that the solution involves the h files, but I'm not sure. Note that I'm trying to do a whole-brain analysis here-I know how to extract betas from functionally and structurally defined ROIs, but I don't know how to do this for the whole brain. Any help will be greatly appreciated. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Possible to pass 2 identical analyses but with different names to intergroupavg-sess?
Dear FreeSurfers, I have two groups (patients vs. controls) whose data I'd like to compare using intergroupavg-sess. Here's the problem: I ran identical analyses on the two groups, but they were named differently (e.g., "control_analysis" vs "patient_analysis"). Is there a way to run intergroupavg-sess without having to either re-name or re-run one of these analyses? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Problem concerning maximum values from mri_volcluster
Dear FreeSurfers, I'm getting odd results from mri_volcluster-the max voxel listed for a given cluster often does not appear to actually be the max in that cluster. This most often appears to happen with small clusters and negative significance values. Below is an example made with abs threshold = 3 and minsizevox = 12 (note that I'm plotting the output from mri_volcluster here, not the raw data, so all the depicted voxels have passed the threshold/cluster requirement). The cursor is at the max voxel as listed by mri_volcluster (significance value is -3.31). However, as can be seen in the example, there is a more extreme/significant value just two voxels over (laterally)-the value there is -4.03. Below is a second example from the same analysis. In this case, I have the cursor on a voxel whose significance value is -5.39. The problem is that mri_volcluster does not list a max voxel with such a significant value-the largest (negative) significance value listed is -4.09. When I first saw things like this I was looking at the raw data, and assumed I was seeing highly significant voxels that were not part of a large enough cluster to meet my minimum voxel size requirement. But the plots shown here were outputted by mri_volcluster using those thresholds (12 voxels, thmin = 3), so that can't be the problem. Am I doing something incorrect here and/or mis-reading the results of mri_volcluster? Any thoughts/advice would be appreciated. I have seen a few cases of this, not just the ones I'm showing here. Again, it seems to come up most frequently for smaller clusters and with negative significance values, although that just may be when it's most obvious to me. Here's the command I used to generate the output for the examples: mri_volcluster --in FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/Rcue_v_RSF/sig --in_type bfloat --reg FPP_HiRisk_MC_375/bold/FPP_MCReg_8_23/tal-rfx/register.dat --thmin 3 --minsizevox 12 --out Test_FPPHiRisk_MC375_Rc_v_RSF --out_type bfloat Thanks in advance. Dan Dillon Affective Neuroscience Lab Harvard University <><>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Volume of sub-cortical structures
Dear FreeSurfers, Hopefully a very easy question . . . I want to compare the volume of subcortical structures in two groups of subjects. All I need to do that is the volume information contained in aseg.stats, right? Just want to double-check before I get started. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Another talairach question . . .
Dear FreeSurfers, In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz. I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue? Thanks in advance, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Another talairach question . . .
Wonderful, thanks. DD -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nick Schmansky Sent: Thursday, November 29, 2007 5:19 PM To: Dan Dillon Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Another talairach question . . . Dan, Include the flag: -notal-check and this will skip the talairach failure detection stage. Nick On Thu, 2007-11-29 at 16:57 -0500, Dan Dillon wrote: > Dear FreeSurfers, > > > > In the course of checking my skull-strips I discovered that one of my > subjects does not have a T1.mgz because they did not pass the > automatic Talairach failure detection. I checked the transformation > with tkregister2 and -fstal, and it actually looks quite good; the > brain is tilted, but the Talairach brain follows the tilt nicely. > Nonetheless, to move things forward I made a few small edits and saved > the registration. I then re-ran autorecon1 using the -notalairach > option (at the end of the command line) in order to make use of my > edits. However, I got the exact same error back-Talairach > transformation ***FAILED***--and consequently there's no T1.mgz. > > > > I thought that by specifying -notalairach at the end of the command > line while running autorecon1, I would be bypassing the Talairach > detector and thus would be able to avoid this problem, but I'm > obviously wrong. How do I make use of my edited Talairach and get > autorecon1 to continue? > > > > Thanks in advance, > > > > Dan Dillon, Ph.D. > > Post-doctoral Fellow > > Affective Neuroscience Lab > > Dept. of Psychology, Harvard University > > Phone: (617) 495-1889 > > E-mail: [EMAIL PROTECTED] > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error encountered while running selxavg3
Dear FreeSurfers, On my maiden voyage with selxavg3, I've encoutered an error and could use some help. After processing several subjects successfully, selxavg3 quit unexpectedly. Here is the exact message: Warning: matrix is singular to working precision > In fast_selxavg3 at 208 ntptot = 666, nX = 31, DOF = 635 ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 235 XCond = cond(XtX); Can anyone help me track down the source of this error and/or suggest a fix? Also, in the course of reviewing the error I saw the following notice: INFO: Key -timeoffset unrecognized, line 7, skipping I have the "timeoffset" argument set to half a TR in my mkanalysis step because I included slicetime correction during preprocessing. Does selxavg3 not recognize this option? Thanks in advance for any help you can provide. Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question about brain masking
Dear FreeSurfers, I'm having some trouble with my brain masks. Below I have inserted a subject's T1.mgz and brain.nii overlay (made with preproc-sess). As you can see, the mask goes well beyond the boundaries of the brain. Any ideas what could cause this-perhaps noisy functional scans? The majority of my subjects' masks look like this. Should I worry about this? My brainmask.mgz files are all fine, and I can use those to mask out voxels for visualization purposes-Do I need to be concerned if my brain.nii volumes look this way? Would I fix by running mkbrainmask-sess and tweaking the "-threshold" argument? Thanks! Dan Dillon Affective Neuroscience Lab Harvard University <><>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_convert problem while unpacking functionals
Dear FreeSurfers, Our group has encountered an error while unpacking the first set of data we acquired on Bay 2 since the upgrade. Here's our command line: unpacksdcmdir -src 07120620/ -targ . -generic -scanonly SUBJ.out We then modify the .out file from 1localizer ok 512 512 3 1 74858975 2 AAScout ok 128 128 128 2 74859004 3T1_MPRAGE_sag ok 256 256 128 1 74856609 4 gre_2d_2mm ok 256 256 55 1 74855396 5 gre_2d_2mm ok 256 256 55 1 74852997 6 field_mapping_2mmthickness ok 128 128 35 2 74853893 7 field_mapping_2mmthickness ok 128 128 35 1 74851708 8 ep2d_t1w ok 64 64 35 1 74848994 9 epzshim_cjw02_nonalternat ok 64 64 35 222 74849554 10 epzshim_cjw02_nonalternat ok 64 64 35 222 74846612 11 epzshim_cjw02_nonalternat ok 64 64 35 222 74843672 12 epzshim_cjw02_nonalternat ok 64 64 35 222 74837495 to 3 T1_MPRAGE_sag COR T1_MPRAGE 8 ep2d_t1w bshort f 9 epzshim_cjw02_nonalternat bshort f 10 epzshim_cjw02_nonalternat bshort f 11 epzshim_cjw02_nonalternat bshort f 12 epzshim_cjw02_nonalternat bshort f and save as SUBJ.cfg Next command line is: unpacksdcmdir -src 07120620/ -targ .. -cfg SUBJ.cfg -fsfast We get this error when it encounters the first functional run: - Run 9 - Mon Dec 10 12:43:27 EST 2007 9 epzshim_cjw02_nonalternat bshort f ERROR: mri_convert child process exited abnormally We've re-run the second unpack command after putting different functional runs (or even single functional runs) in the first position processed, and the same error message occurs each time. We've also tried the process on functional runs that do not have a z-shim (thought that might be causing trouble), but the error still comes up. Any ideas? Thanks in advance. Dan Dillon (on behalf of Elena Goetz) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Obtaining cortical parcellations
Dear FreeSurfers, I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-autorecon3-parcellation"? I am running version 4.0.1. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Odd tkmedit behavior
Dear FreeSurfers, I have overlaid group data on the fsaverage brain, and find that when I type Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas what could be causing this trouble? Thanks! Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Odd tkmedit behavior
Into the "tkmedit tools", the second window under "Cursor" . . . I have a sig map overlaid and am checking the output of mri_volcluster by typing the coordinates in and verifying significance values . . . when I the coordinates of a cluster in, the cursor jumps to a nearby position and the Talairach coordinates change slightly from what I entered. -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 03, 2008 3:24 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior What do you mean that type Tal coords into tkmedit? Dan Dillon wrote: Dear FreeSurfers, I have overlaid group data on the fsaverage brain, and find that when I type Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas what could be causing this trouble? Thanks! Dan Dillon _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Odd tkmedit behavior
Okay, sounds good-thanks. DD -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 03, 2008 3:44 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior We're tracking it down, but it appears to be in the bowels of our TCL code, so it could be a while. Dan Dillon wrote: Into the "tkmedit tools", the second window under "Cursor" . . . I have a sig map overlaid and am checking the output of mri_volcluster by typing the coordinates in and verifying significance values . . . when I the coordinates of a cluster in, the cursor jumps to a nearby position and the Talairach coordinates change slightly from what I entered. -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 03, 2008 3:24 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior What do you mean that type Tal coords into tkmedit? Dan Dillon wrote: Dear FreeSurfers, I have overlaid group data on the fsaverage brain, and find that when I type Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas what could be causing this trouble? Thanks! Dan Dillon _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Odd tkmedit behavior
Thanks Bruce! DD -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: Tuesday, March 04, 2008 10:54 AM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Odd tkmedit behavior Hi Dan, I managed to track this down and fix it. Note that the cursor will move a bit to the center of the voxel with that tal coord, but not much. The fix will be in the next stable release (soon), or you can get a dev version from Nick. cheers, Bruce On Mon, 3 Mar 2008, Dan Dillon wrote: > Dear FreeSurfers, > > > > I have overlaid group data on the fsaverage brain, and find that when I type > Talairach coordinates into tkmedit (e.g., 9.90 -36.64 -14.15), the cursor > jumps to a nearby but different location (e.g., 9.8 -36.1 -10.1). Any ideas > what could be causing this trouble? > > > > Thanks! > > > > Dan Dillon > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Question re: extracting functional data from cortical ROIs
I have a question about extracting functional data from structurally defined cortical labels. Here's what I'm doing: 1) Run a gammafit analysis; 2) Define cortical ROIs by using mri_annotation2label to make labels from aparc.annot; 3) Define sub-cortical ROIs by using mri_cor2label to make labels from aseg.mgz; 4) Extract functional data from labels using func2roi-sess; 5) Summarize the data with roisummary-sess. I usually view the cortical ROIs on the inflated (or pial) surface and the subcortical ROIs in the volume, and they usually look great. But when I view the cortical labels in the volume, they seem to consist of a 1-voxel thick strip hugging the white matter; they don't seem to cover the gray matter at all. Does this mean that I am extracting functional data from a 1-voxel thick strip (!), or am I just mis-understanding something about how a cortical label appears in the volume? Also, I know that "white" is the default surface in mri_annotation2label, but if I switch to "pial", make a label, and view it in the volume, it still looks like a 1-voxel thick strip, just around the outside edge of the gray matter (instead of around the inside edge if I use "white" as the surface). My simple mind wonders why these cortical labels-which look great on the inflated brain-don't cover the region between the pial and white surfaces (i.e., the gray matter) in the volume. Am I making a basic error here? If so, what do I need to do to extract functional data from cortically-defined ROIs? I am running version 4.0.2. Thanks! Dan D. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Question re: extracting functional data from cortical ROIs
Hi Doug. So if I'm understanding you, the 1mm3 voxel overlaps the larger (3 x 3 x 3 mm) functional voxel and so when I pull out the functional data it comes from the entire functional voxel? Is the combination of mri_annotation2label and func2roi-sess a common way to extract data from cortical ROIs? Is there a set of flags that generally works well that I should use to make sure I'm getting data from all the gray matter? Thanks! Dan -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, March 17, 2008 4:56 PM To: Dan Dillon Cc: 'Freesurfer Mailing List' Subject: Re: [Freesurfer] Question re: extracting functional data from cortical ROIs Yes, it is that 1mm3 voxel on the white (or pial) surface. For sampling into the functional volume, this is usually not an issue as the functional voxels are generally much bigger. You can change the cortical sampling depth by running mri_label2label with --projfrac (eg, --projfrac 0.5 for midway between the white and pial). doug Dan Dillon wrote: I have a question about extracting functional data from structurally defined cortical labels. Here's what I'm doing: 1) Run a gammafit analysis; 2) Define cortical ROIs by using mri_annotation2label to make labels from aparc.annot; 3) Define sub-cortical ROIs by using mri_cor2label to make labels from aseg.mgz; 4) Extract functional data from labels using func2roi-sess; 5) Summarize the data with roisummary-sess. I usually view the cortical ROIs on the inflated (or pial) surface and the subcortical ROIs in the volume, and they usually look great. But when I view the cortical labels in the volume, they seem to consist of a 1-voxel thick strip hugging the white matter; they don't seem to cover the gray matter at all. Does this mean that I am extracting functional data from a 1-voxel thick strip (!), or am I just mis-understanding something about how a cortical label appears in the volume? Also, I know that "white" is the default surface in mri_annotation2label, but if I switch to "pial", make a label, and view it in the volume, it still looks like a 1-voxel thick strip, just around the outside edge of the gray matter (instead of around the inside edge if I use "white" as the surface). My simple mind wonders why these cortical labels-which look great on the inflated brain-don't cover the region between the pial and white surfaces (i.e., the gray matter) in the volume. Am I making a basic error here? If so, what do I need to do to extract functional data from cortically-defined ROIs? I am running version 4.0.2. Thanks! Dan D. _ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Citation for FSFAST
Hi Doug. What's the preferred citation/reference for FSFAST? Dan Dillon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Possible to regress whole-brain functional data against continuous variables in the volume?
Hi FreeSurfers. Is it possible to regress functional data against a continuous variable in the volume? I'm analyzing a reward processing study that activates sub-cortical and cortical regions, and I'd like to regress those data against a continuous measure of depressive symptoms administered to each participant. I understand the basic fsgd/mri_glmfit approach from the FS tutorial, but I want to stay in the volume in order to examine sub-cortical structures (e.g., nucleus accumbens). Is this possible? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
