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30091 discussions

slice timing
by Meryem Ayse Yucel 01 Apr '13

01 Apr '13

Doug, I use preproc-sess 's -stc up option to time correct my slices. I only have 6 slices. Donald, I am not calculating absolute CBF values using the calibration scan. I pre-process the data and then either surround-subtract or just subtract tag from control to get CBF, would it still be a problem to use slice time correction? Thanks, Meryem Message: 11 Date: Fri, 29 Mar 2013 13:40:42 -0400 From: "MCLAREN, Donald" <mclaren.donald(a)gmail.com> Subject: Re: [Freesurfer] slice timing To: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAKwrF_XJfg=PRTm2htZ12FN74VtP2qGzqffAGKeZBJO+pXDrQQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" If you are using ASL, you do not want to use Slice timing. You must compute the CBF maps and keep the slice timing intact. Removing the time delay between slices will lead to the wrong CBF values as the CBF equations have the time delay in the equation. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Fri, Mar 29, 2013 at 1:08 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > what are you using to do STC? I think by default FSL will move it to the > middle slice, but there is probably a way to make take into account the > fact that the slices are not uniform over the TR. You should contact the > list of the software you are using to get a definative answer. > doug > > > On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote: > > Hi, > > > > I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am > > wondering when I do slice time correction does that move all slices to > the > > mid of TR that is 1.5 s prior in time or, it moves them to the timing of > > the mid slice, which would be the mid of image acquisition aorund 0.6 sec > > prior in time with respect to the end of TR. > > > > Thank you, > > > > Meryem > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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More QDEC questions
by Tudor Popescu 01 Apr '13

01 Apr '13

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: - why does QDEC only provide the volume of *subcortical* structures under StatsDataImport/aseg.volume, when the automatic GM/WM segmentation is done for the entire brain, not just for subcortical regions? - how are the volume measurements provided in aseg.volume different from the ones done obtained with a VBM analysis? - why is *volume *the result of *segmentation *(aseg.volume) whereas *thickness *derives from *parcelation *(rh.aparc.thickness)? Is it not the case that both operations (segmentation+parcellation) are necessary to calculate volume as well as thickness? - how is a QDEC thickness analysis different from a regular AN(C)OVA in which you are interested in main and interaction effects of the IVs on the DV? I ask this because some of the questions that appear in QDEC's Analysis Results tab – e.g. "is the correlation between (DV) and (IV) different from zero?" – would not (I think) be directly answerable by an ANOVA - would the same type of ANOVA done by QDEC be doable by extracting the values of the DV for each subject (using e.g. *aseg.volume*) and then doing the ANOVA in e.g. SPSS? If so, when would you do one versus the other? - why is it that only continuous factors (e.g. age) can be taken in the analysis as nuisance factors, when discrete variables (e.g. gender) might also be irrelevant for a particular analysis and thus belong to the Nuisance Factor list? Many thanks in advance!! Tudor

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MAking cuts using tksurfer
by Anupa AV 01 Apr '13

01 Apr '13

Dear All, How to explore the "cut" tools in freesurfer using tksurfer? I'd like to make a cut along the vertex on the cortical surface (say, inflated) to divide medial and lateral components. How to do it after loading DKatlas labels and I want to cut along the vertex to divde medial and lateral components.? Thanks in advance for your response.

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FS 5.2 asegstats2table is not found or is too small to be a valid stats file error
by Salil Soman 31 Mar '13

31 Mar '13

Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files * Any suggestions on what I am doing incorrectly? I would like to extract all of the statistics in aseg.stats into a single row per subject to facilitate additional analysis in other programs. Any suggestions on how to accomplish this would be much appreciated. Thank you. -S* *

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mri_glmfit-sim doesn't recognize --label flag
by Yizhou Ma 31 Mar '13

31 Mar '13

Dear freesurfer experts, I'm doing small volume correction for multiple comparison. However, when I run "mri_glmfit-sim" with "--label mylabelfile", I got the error that "--label unrecognizable". I use "mri_glmfit-sim --help" to see the help information but there is no information regarding "--label" or "--mask". May I know why this? P.S. I use FS510. I have run mri_glmfit-sim successfully without a mask. Thanks, Cherry

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tractstats@table output oddity
by Jon Wieser 31 Mar '13

31 Mar '13

I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list "fmajor_file_list.txt" it produced the output file "fmajor_table.txt" (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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denominator of the t-test in fsfast?
by Alex Kell 31 Mar '13

31 Mar '13

freesurfers, i have a question about how t-tests are computed in fsfast. so t = ces/sqrt(cesvar), but how exactly is cesvar calculated? i thought it would be: cesvar = variance_of_residual * c*(X' * X)^-1*c' where X is the stim matrix and c is the contrast vector and ' denotes transpose two questions: 1. i tried computing cesvar myself, but it is not the equation above (for the one subject i was playing with, cesvar was ~1.5x the above equation). what is the equation that is used? 2. intuitively, the second half of that [ c*(X' * X)^-1*c ] penalizes for correlations in your stimulus matrix, particularly for those relevant to your contrast. is that a good way to think about it? thanks in advance! alex

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specifying random effects in LME (Linear Mixed Effects models)
by Lalonde, Francois (NIH/NIMH) [E] 29 Mar '13

29 Mar '13

I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892

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Set up data for longitudinal processing
by Lukas.Scheef＠ukb.uni-bonn.de 29 Mar '13

29 Mar '13

Hi folks, sorry it's me again with a very basic question. What is the best way to import longitudinal data? recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT or recon-all -i /path/T1A.nii FIRSTSUBJECT_A recon-all -i /path/T1A.nii FIRSTSUBJECT_B I tend to use the second choice because otherwise I would have no idea how to distinguish between SUBJECT-ID and TimepointID later on in the processing stream. Best whises, Luke

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FS5.2: selxavg3-sess error
by tapsya＠nmr.mgh.harvard.edu 29 Mar '13

29 Mar '13

Dear Doug, I am trying to analyze fMRI data where TR = 1.2 secs. For several subjects the analysis works as expected, but for about half of the subjects when I try to execute the command selxavg3-sess terminates with the following error: "OLS Beta Pass run 1 t= 0.0 ERROR: TR mismatch between analysis and data analysis TR = 1.2, data TR = 1.56" I checked the *nii header information and all indicate TR = 1.2 sec. I am not sure why I get the error. Please advise. Thanks! Wishes, Tapsya FS-FAST version: 5.2 Machine: adapt

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